Re: [Freesurfer] mri_convert: Segmentation fault (core dumped) synthsr scan

[KennethSPrice]

External Email - Use Caution

I looked through the thread and downloaded VirtualBox. Freesurfer 5.1 
installation was working fine but mounting my drive and sharing folders 
required so many libraries which are now defunct, it just wasn't worth it. I 
wrangled with the machine for a while but it seems easier to just process 
everything with freesurfer 7.4.

Thanks,
K
--- Original Message ---
On Monday, September 18th, 2023 at 8:02 AM, Huang, Yujing 
 wrote:

> External Email - Use Caution
>
> You are using Freesurfer 5.1 
> (freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0). I’m wondering if it is 
> software compatibility issue.
>
> There are suggestions on how to run Freesurfer 5.1 from container in this 
> posting - [MailScanner has detected a possible fraud attempt from 
> "secure-web.cisco.com" claiming to be 
> https://secure-web.cisco.com/18JSemI8UZisRAbamkAD4iEpeHnPbUto45vp33zIyv6IxlxH6YY_ccXNVq1bmims4D73UhRQQc55skHaxr7mL7bmo19VXhughEQHs2oC_SgCBJM6Pspz18oq8ETY0yiZ1gy_iRlnnHVgzkRWKKBU7p8dUY_RNJ_fp0F9C4ruTUINzQs8aE-tbwUm-j7sbo67BsA1NUuAarLEtmv7TBc0UASWbPhDkfweJtDJ3L6B75NnbOyr3i0vR2CYwEgegY0UcJ8KS_XX7uqmR6GcFKyqky_Tz-Zpj_rxSLW8dM8V85Hz-FiK6aR0GUgu-JXHRsTQE/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg74552.html](https://secure-web.cisco.com/1zoee5Wuv_DvRaT0fpKqBwycBeglhqic772BD4C6VpO6izm3ko3HbKPFAhhiSvHUnH2VQsVbbE6SCsil2t_uZiXawtT72CtBfi8VIAFZuWUn25D4ubxeaap7woc9mG9Yy1Wu1Es0agG-DTknpF_Wehz_xUywjWQyLGqahiHTWbSDXkJDIkMD-VXedp_TMcIAgjTWyYdyMA1Vy2cRruqatwVaE03hCpnXnjrovVfhMKBXrWCBilDshe2qF6UT2gEt4/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg74552.html)
>
> Hope this helps.
>
> Best,
>
> Yujing
>
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  On Behalf Of KennethSPrice
> Sent: Sunday, September 17, 2023 11:35 AM
> To: Freesurfer support list 
> Subject: Re: [Freesurfer] mri_convert: Segmentation fault (core dumped) 
> synthsr scan
>
> External Email - Use Caution
>
> I've set the coredumpsize to unlimited, and still get the same error. Could 
> it be something with the installation?
>
> build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0
>
> Linux DESKTOP-MRI 4.4.0-19041-Microsoft #3393-Microsoft Mon Aug 14 14:52:00 
> PST 2023 x86_64 x86_64 x86_64 GNU/Linux
>
> cputime unlimited
>
> filesize unlimited
>
> datasize unlimited
>
> stacksize 8192 kbytes
>
> coredumpsize unlimited
>
> memoryuse unlimited
>
> vmemoryuse unlimited
>
> descriptors 1024
>
> memorylocked 64 kbytes
>
> maxproc 7823
>
> maxlocks unlimited
>
> maxsignal 7823
>
> maxmessage 819200
>
> maxnice 0
>
> maxrtprio 0
>
> maxrttime unlimited
>
> total used free shared buff/cache available
>
> Mem: 16643620 4264632 12149636 17720 229352 12245256
>
> Swap: 29192228 0 29192228
>
> --- Original Message ---
> On Saturday, September 16th, 2023 at 9:49 PM, fsbuild  
> wrote:
>
>> External Email - Use Caution
>>
>> Hello Ken,
>>
>> The output from your linux shell limits in the log show the following,
>>
>> cputime unlimited
>>
>> filesize unlimited
>>
>> datasize unlimited
>>
>> stacksize 8192 kbytes
>>
>> coredumpsize 0 kbytes
>>
>> memoryuse unlimited
>>
>> vmemoryuse unlimited
>>
>> descriptors 1024
>>
>> memorylocked 64 kbytes
>>
>> maxproc 7823
>>
>> maxlocks unlimited
>>
>> maxsignal 7823
>>
>> maxmessage 819200
>>
>> maxnice 0
>>
>> maxrtprio 0
>>
>> maxrttime unlimited
>>
>> I would set at least coredumpsize to something non-zero so you can at least 
>> get a core file saved that could be looked at. By default the limits on my 
>> Ubuntu 22 system are:
>>
>> $ ulimit -a
>>
>> real-time non-blocking time(microseconds, -R) unlimited
>>
>> core file size(blocks, -c) unlimited
>>
>> data seg size (kbytes, -d) unlimited
>>
>> scheduling priority (-e) 0
>>
>> file size (blocks, -f) unlimited
>>
>> pending signals (-i) 378881
>>
>> max locked memory (kbytes, -l) 64
>>
>> max memory size (kbytes, -m) unlimited
>>
>> open files(-n) 1048576
>>
>> pipe size(512 bytes, -p) 8
>>
>> POSIX message queues (bytes, -q) 819200
>>
>> real-time priority(-r) 0
>>
>> stack size(kbytes, -s) 8192
>>
>> cpu time (seconds, -t) unlimited
>>
>> max user processes(-u) unlimited
>>
>> virtual memory(kbytes, -v) unlimited
>>
>> file locks(-x) unlimited
>>
>> You

Re: [Freesurfer] mri_convert: Segmentation fault (core dumped) synthsr scan

[Huang, Yujing]

External Email - Use Caution

You are using Freesurfer 5.1 
(freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0).  I’m wondering if it is 
software compatibility issue.

There are suggestions on how to run Freesurfer 5.1 from container in this 
posting - 
https://secure-web.cisco.com/1zoee5Wuv_DvRaT0fpKqBwycBeglhqic772BD4C6VpO6izm3ko3HbKPFAhhiSvHUnH2VQsVbbE6SCsil2t_uZiXawtT72CtBfi8VIAFZuWUn25D4ubxeaap7woc9mG9Yy1Wu1Es0agG-DTknpF_Wehz_xUywjWQyLGqahiHTWbSDXkJDIkMD-VXedp_TMcIAgjTWyYdyMA1Vy2cRruqatwVaE03hCpnXnjrovVfhMKBXrWCBilDshe2qF6UT2gEt4/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg74552.html

Hope this helps.

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of KennethSPrice
Sent: Sunday, September 17, 2023 11:35 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] mri_convert: Segmentation fault (core dumped) synthsr 
scan


External Email - Use Caution
I've set the coredumpsize to unlimited, and still get the same error. Could it 
be something with the installation?

build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0
Linux DESKTOP-MRI 4.4.0-19041-Microsoft #3393-Microsoft Mon Aug 14 14:52:00 PST 
2023 x86_64 x86_64 x86_64 GNU/Linux
cputime  unlimited
filesize unlimited
datasize unlimited
stacksize8192 kbytes
coredumpsize unlimited
memoryuseunlimited
vmemoryuse   unlimited
descriptors  1024
memorylocked 64 kbytes
maxproc  7823
maxlocks unlimited
maxsignal7823
maxmessage   819200
maxnice  0
maxrtprio0
maxrttimeunlimited

  totalusedfree  shared  buff/cache   available
Mem:   16643620 426463212149636   17720  22935212245256
Swap:  29192228   029192228
--- Original Message ---
On Saturday, September 16th, 2023 at 9:49 PM, fsbuild 
mailto:fsbu...@contbay.com>> wrote:



External Email - Use Caution
Hello Ken,

The output from your linux shell limits in the log show the following,

cputime  unlimited
filesize unlimited
datasize unlimited
stacksize8192 kbytes
coredumpsize 0 kbytes
memoryuseunlimited
vmemoryuse   unlimited
descriptors  1024
memorylocked 64 kbytes
maxproc  7823
maxlocks unlimited
maxsignal7823
maxmessage   819200
maxnice  0
maxrtprio0
maxrttimeunlimited

I would set at least coredumpsize to something non-zero so you can at least get 
a core file saved that could be looked at.   By default the limits on my Ubuntu 
22 system are:


$ ulimit -a

real-time non-blocking time  (microseconds, -R) unlimited

core file size  (blocks, -c) unlimited

data seg size   (kbytes, -d) unlimited

scheduling priority (-e) 0

file size   (blocks, -f) unlimited

pending signals (-i) 378881

max locked memory   (kbytes, -l) 64

max memory size (kbytes, -m) unlimited

open files  (-n) 1048576

pipe size(512 bytes, -p) 8

POSIX message queues (bytes, -q) 819200

real-time priority  (-r) 0

stack size  (kbytes, -s) 8192

cpu time   (seconds, -t) unlimited

max user processes  (-u) unlimited

virtual memory  (kbytes, -v) unlimited

file locks  (-x) unlimited

You can try setting the core file size to unlimited with,

$ ulimit -c unlimited
... then check the value was changed to something > 0 ...
$ ulimit -a

You could increase memory size (and as many shell limits as possible) to 
unlimited to get the max size allowed by the system in the script you use to 
run recon-all, and then try running recon-all  again to see if you can retrieve 
a core dump file.

- R.


On Sep 16, 2023, at 09:55, KennethSPrice 
mailto:kennethspr...@protonmail.com>> wrote:

External Email - Use Caution

OK, I've attached the log file.

--- Original Message ---
On Friday, September 15th, 2023 at 2:59 PM, fsbuild 
mailto:fsbu...@contbay.com>> wrote:


External Email - Use Caution

 It might help if you could send along the crash report as an attachment..

-R.


On Sep 15, 2023, at 14:36, KennethSPrice 
mailto:kennethspr...@protonmail.com>> wrote:

External Email - Use Caution

Update: I tried running recon-all (5.1, ubuntu 18) on a sample MPRAGE scan and 
got the "mri_convert: segmentation fault (core dumped)" error again. Any 
clarity on this issue would be appreciated.

Thanks,
K
--- Original Message ---
On Thursday, September 14th, 2023 at 10:41 PM, KennethSPrice 
mailto:kennethspr...@protonmail.com>> wrote:


Howdy yall,

I ran a subject through synthsr (freesurfer 7.4) and am trying to run the 
output through the freesurfer 5.1 pipeline (the rest of my dataset was 
processed with 5.1). I am getting the error "Segmentation fault (core dumped)" 

Re: [Freesurfer] mri_convert: Segmentation fault (core dumped) synthsr scan

[KennethSPrice]

External Email - Use Caution

I've set the coredumpsize to unlimited, and still get the same error. Could it 
be something with the installation?

build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0
Linux DESKTOP-MRI 4.4.0-19041-Microsoft #3393-Microsoft Mon Aug 14 14:52:00 PST 
2023 x86_64 x86_64 x86_64 GNU/Linux
cputime unlimited
filesize unlimited
datasize unlimited
stacksize 8192 kbytes
coredumpsize unlimited
memoryuse unlimited
vmemoryuse unlimited
descriptors 1024
memorylocked 64 kbytes
maxproc 7823
maxlocks unlimited
maxsignal 7823
maxmessage 819200
maxnice 0
maxrtprio 0
maxrttime unlimited

total used free shared buff/cache available
Mem: 16643620 4264632 12149636 17720 229352 12245256Swap: 29192228 0 29192228
--- Original Message ---
On Saturday, September 16th, 2023 at 9:49 PM, fsbuild  
wrote:

> External Email - Use Caution
>
> Hello Ken,
>
> The output from your linux shell limits in the log show the following,
>
> cputime unlimited
> filesize unlimited
> datasize unlimited
> stacksize 8192 kbytes
> coredumpsize 0 kbytes
> memoryuse unlimited
> vmemoryuse unlimited
> descriptors 1024
> memorylocked 64 kbytes
> maxproc 7823
> maxlocks unlimited
> maxsignal 7823
> maxmessage 819200
> maxnice 0
> maxrtprio 0
> maxrttime unlimited
>
> I would set at least coredumpsize to something non-zero so you can at least 
> get a core file saved that could be looked at. By default the limits on my 
> Ubuntu 22 system are:
>
> $ ulimit -a
>
> real-time non-blocking time(microseconds, -R) unlimited
>
> core file size(blocks, -c) unlimited
>
> data seg size (kbytes, -d) unlimited
>
> scheduling priority (-e) 0
>
> file size (blocks, -f) unlimited
>
> pending signals (-i) 378881
>
> max locked memory (kbytes, -l) 64
>
> max memory size (kbytes, -m) unlimited
>
> open files(-n) 1048576
>
> pipe size(512 bytes, -p) 8
>
> POSIX message queues (bytes, -q) 819200
>
> real-time priority(-r) 0
>
> stack size(kbytes, -s) 8192
>
> cpu time (seconds, -t) unlimited
>
> max user processes(-u) unlimited
>
> virtual memory(kbytes, -v) unlimited
>
> file locks(-x) unlimited
>
> You can try setting the core file size to unlimited with,
>
> $ ulimit -c unlimited
> ... then check the value was changed to something > 0 ...
> $ ulimit -a
>
> You could increase memory size (and as many shell limits as possible) to 
> unlimited to get the max size allowed by the system in the script you use to 
> run recon-all, and then try running recon-all again to see if you can 
> retrieve a core dump file.
>
> - R.
>
>> On Sep 16, 2023, at 09:55, KennethSPrice  
>> wrote:
>>
>> External Email - Use Caution
>>
>> OK, I've attached the log file.
>>
>> --- Original Message ---
>> On Friday, September 15th, 2023 at 2:59 PM, fsbuild  
>> wrote:
>>
>>> External Email - Use Caution
>>>
>>> It might help if you could send along the crash report as an attachment..
>>>
>>> -R.
>>>
 On Sep 15, 2023, at 14:36, KennethSPrice  
 wrote:

 External Email - Use Caution

 Update: I tried running recon-all (5.1, ubuntu 18) on a sample MPRAGE scan 
 and got the "mri_convert: segmentation fault (core dumped)" error again. 
 Any clarity on this issue would be appreciated.

 Thanks,
 K
 --- Original Message ---
 On Thursday, September 14th, 2023 at 10:41 PM, KennethSPrice 
  wrote:

> Howdy yall,
>
> I ran a subject through synthsr (freesurfer 7.4) and am trying to run the 
> output through the freesurfer 5.1 pipeline (the rest of my dataset was 
> processed with 5.1). I am getting the error "Segmentation fault (core 
> dumped)" during the mri_convert step. Any suggestions?
>
> Thanks,
> Ken

 ___
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 Freesurfer@nmr.mgh.harvard.edu
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>> https://secure-web.cisco.com/1G2WVoZQh8QnLdPMLpSy6ZFKJkxwqlcIbB78ZeuCKMWoQ3EGF4hJ-r8jgrRtARq2I8ydEblD0Dzi5lElK2rA4W_F7399TAtOXIwMVfF_3vCqd8-xlfzvx1N69PyLfU_ti4uOT7shoqKAjMEOgPxQDBCMqTGNjuRH4bNFgBp5FDnPYeAe4A7ZRSIbFQ3R2LX9g85jWMhg8eL1bmb_aNGPG4I2uEC0iuOLG6Pj-4COlUKw01YQgKq0QUWaoH-irFZuXEpJiEWMkCXlasAJJFfGbdNB-W7vu0b-UPL-sKq7wtkxOQpaxllN5OeBx2UPEGdUDwBU14Vjw2gq07tJ8sefPXg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] mri_convert: Segmentation fault (core dumped) synthsr scan

[fsbuild]

External Email - Use Caution

Hello Ken,
The output from your linux shell limits in the log show the following,
cputime   unlimitedfilesize  
unlimiteddatasize  unlimitedstacksize  8192 
kbytescoredumpsize 0 kbytesmemoryuse  unlimitedvmemoryuse 
unlimiteddescriptors 1024memorylocked 64 kbytesmaxproc 
  7823maxlocks  unlimitedmaxsignal 
 7823maxmessage 819200maxnice   
0maxrtprio  0maxrttime  unlimited
I would set at least coredumpsize to something non-zero so you can at least get 
a core file saved that could be looked at. By default the limits on 
my Ubuntu 22 system are:
$ ulimit -areal-time non-blocking time (microseconds, -R) unlimitedcore 
file size   (blocks, -c) 
unlimiteddata seg size
(kbytes, -d) unlimitedscheduling priority  
   (-e) 0file size   
   (blocks, -f) unlimitedpending signals
   (-i) 378881max locked memory 
 (kbytes, -l) 64max memory size   
(kbytes, -m) unlimitedopen files  
   
(-n) 1048576pipe size
(512 bytes, -p) 8POSIX message queues (bytes, -q) 
819200real-time priority
 (-r) 0stack size
 (kbytes, -s) 8192cpu time   
   (seconds, -t) unlimitedmax user processes  
   (-u) unlimitedvirtual 
memory   (kbytes, -v) 
unlimitedfile locks
 (-x) unlimited
You can try setting the core file size to unlimited with,
$ ulimit -c unlimited... then check the value was changed to something  0 
...$ ulimit -a
You could increase memory size (and as many shell limits as possible) to 
unlimited to get the max size allowed by the system in the script you use to 
run recon-all, and then try running recon-all again to see if you can 
retrieve a core dump file.
- R.

On Sep 16, 2023, at 09:55, KennethSPrice kennethspr...@protonmail.com 
wrote:External Email - Use 
CautionOK, I've attached the 
log file.--- Original Message ---On Friday, September 15th, 2023 
at 2:59 PM, fsbuild fsbu...@contbay.com 
wrote:External Email - Use 
CautionIt might help if 
you could send along the crash report as an attachment..-R.On Sep 15, 2023, at 
14:36, KennethSPrice kennethspr...@protonmail.com 
wrote:External Email - Use 
CautionUpdate: I tried running 
recon-all (5.1, ubuntu 18) on a sample MPRAGE scan and got the "mri_convert: 
segmentation fault (core dumped)" error again. Any clarity on this issue would 
be appreciated.Thanks,K--- Original Message ---On Thursday, 
September 14th, 2023 at 10:41 PM, KennethSPrice 
kennethspr...@protonmail.com wrote:Howdy yall,I ran a subject through 
synthsr (freesurfer 7.4) and am trying to run the output through the freesurfer 
5.1 pipeline (the rest of my dataset was processed with 5.1). I am getting the 
error "Segmentation fault (core dumped)" during the mri_convert step. Any 
suggestions?Thanks,Ken___Freesurfer
 mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferrecon-all.log___Freesurfer
 mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] mri_convert: Segmentation fault (core dumped) synthsr scan

[KennethSPrice]

External Email - Use Caution

OK, I've attached the log file.

--- Original Message ---
On Friday, September 15th, 2023 at 2:59 PM, fsbuild  wrote:

> External Email - Use Caution
>
> It might help if you could send along the crash report as an attachment..
>
> -R.
>
>> On Sep 15, 2023, at 14:36, KennethSPrice  
>> wrote:
>>
>> External Email - Use Caution
>>
>> Update: I tried running recon-all (5.1, ubuntu 18) on a sample MPRAGE scan 
>> and got the "mri_convert: segmentation fault (core dumped)" error again. Any 
>> clarity on this issue would be appreciated.
>>
>> Thanks,
>> K
>> --- Original Message ---
>> On Thursday, September 14th, 2023 at 10:41 PM, KennethSPrice 
>>  wrote:
>>
>>> Howdy yall,
>>>
>>> I ran a subject through synthsr (freesurfer 7.4) and am trying to run the 
>>> output through the freesurfer 5.1 pipeline (the rest of my dataset was 
>>> processed with 5.1). I am getting the error "Segmentation fault (core 
>>> dumped)" during the mri_convert step. Any suggestions?
>>>
>>> Thanks,
>>> Ken
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://secure-web.cisco.com/1n7fWOKSqI2VgPx35GDySYUjhvmIyBhf7FZreHbZZJS85Js0ir9bAdH9TSGhzmF25NdqiznSd27ygKVfTXb4XAHOXsyK5RWtBQkPNrOookPK6vLnvjbB1ShzSpqasaDrPBMaSFZBzb6XWC-L7JVJ1XFLi5491qO1VTcoYiT7Clp2PG4B2Sx_lLu_Um31g-Zu3mAGBgzo9C2ihGhL2ZsmOxYpylA_V34KCgCqbjtpzNRChwdDiGodk71jHdw_4_BfgjcaPHiVxhOO27vyg59nCvgT0BsXa6VuGip75gImbttHrWyMXEFm0CnDBFDab9Ilnei5iqjQ78C5E_F3MkeZD-g/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2FfreesurferSat Sep 16 09:44:02 EDT 2023
/mnt/c/users/mri/desktop/2015/2020
/usr/local/freesurfer/bin/recon-all
-all -i 2020gre.nii -s 2020
subjid 2020
setenv SUBJECTS_DIR /mnt/c/users/mri/desktop/2015
FREESURFER_HOME /usr/local/freesurfer
Actual FREESURFER_HOME /usr/local/freesurfer
build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0
Linux DESKTOP-MRI 4.4.0-19041-Microsoft #3393-Microsoft Mon Aug 14 14:52:00 PST 
2023 x86_64 x86_64 x86_64 GNU/Linux
cputime  unlimited
filesize unlimited
datasize unlimited
stacksize8192 kbytes
coredumpsize 0 kbytes
memoryuseunlimited
vmemoryuse   unlimited
descriptors  1024 
memorylocked 64 kbytes
maxproc  7823 
maxlocks unlimited
maxsignal7823 
maxmessage   819200 
maxnice  0 
maxrtprio0 
maxrttimeunlimited

  totalusedfree  shared  buff/cache   available
Mem:   16643620 436721612047052   17720  22935212142672
Swap:  29192228   029192228


program versions used
$Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 nicks Exp $
$Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $
mri_convert -all-info 
ProgramName: mri_convert  ProgramArguments: -all-info  ProgramVersion: $Name: 
stable5 $  TimeStamp: 2023/09/16-13:44:03-GMT  BuildTimeStamp: May 26 2011 
08:56:44  CVS: $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $  
User: ken  Machine: DESKTOP-MRI  Platform: Linux  PlatformVersion: 
4.4.0-19041-Microsoft  CompilerName: GCC  CompilerVersion: 30400 
FLIRT version 5.5
$Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $
mri_convert --version 
stable5
ProgramName: tkregister2_cmdl  ProgramArguments: --all-info  ProgramVersion: 
$Name: stable5 $  TimeStamp: 2023/09/16-13:44:04-GMT  BuildTimeStamp: May 26 
2011 08:56:44  CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve 
Exp $  User: ken  Machine: DESKTOP-MRI  Platform: Linux  PlatformVersion: 
4.4.0-19041-Microsoft  CompilerName: GCC  CompilerVersion: 30400 
Program nu_correct, built from:
Package MNI N3, version 1.10, compiled by nicks@minerva 
(x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37
ProgramName: mri_make_uchar  ProgramArguments: -all-info  ProgramVersion: 
$Name: stable5 $  TimeStamp: 2023/09/16-13:44:04-GMT  BuildTimeStamp: May 26 
2011 08:56:44  CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ 
 User: ken  Machine: DESKTOP-MRI  Platform: Linux  PlatformVersion: 
4.4.0-19041-Microsoft  CompilerName: GCC  CompilerVersion: 30400 
ProgramName: mri_normalize  ProgramArguments: -all-info  ProgramVersion: $Name: 
stable5 $  TimeStamp: 2023/09/16-13:44:05-GMT  BuildTimeStamp: May 26 2011 
08:56:44  CVS: $Id: mri_normalize.c,v 1.73 2011/03/11 20:55:38 fischl Exp $  
User: ken  Machine: DESKTOP-MRI  Platform: Linux  PlatformVersion: 
4.4.0-19041-Microsoft  CompilerName: GCC  CompilerVersion: 30400 
ProgramName: mri_watershed  ProgramArguments: -all-info  ProgramVersion: $Name: 
stable5 $  TimeStamp: 2023/09/16-13:44:05-GMT  BuildTimeStamp: May 26 2011 
08:56:44  CVS: $Id: mri_watershed.cpp,v 1.96 2011/03/16 21:23:49 nicks Exp $  
User: ken  Machine: DESKTOP-MRI  Platform: Linux  PlatformVersion: 
4.4.0-19041-Microsoft  CompilerName: GCC  CompilerVersion: 30400 
ProgramName: mri_gcut  ProgramArguments: -all-info  

Re: [Freesurfer] mri_convert: Segmentation fault (core dumped) synthsr scan

[fsbuild]

External Email - Use Caution

It might help if you could send along the crash report as an attachment.
-R.

On Sep 15, 2023, at 14:36, KennethSPrice kennethspr...@protonmail.com 
wrote:External Email - Use 
CautionUpdate: I tried running 
recon-all (5.1, ubuntu 18) on a sample MPRAGE scan and got the "mri_convert: 
segmentation fault (core dumped)" error again. Any clarity on this issue would 
be appreciated.Thanks,K--- Original Message ---On Thursday, 
September 14th, 2023 at 10:41 PM, KennethSPrice 
kennethspr...@protonmail.com wrote:Howdy yall,I ran a subject through 
synthsr (freesurfer 7.4) and am trying to run the output through the freesurfer 
5.1 pipeline (the rest of my dataset was processed with 5.1). I am getting the 
error "Segmentation fault (core dumped)" during the mri_convert step. Any 
suggestions?Thanks,Ken___Freesurfer
 mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] mri_convert: Segmentation fault (core dumped) synthsr scan

[KennethSPrice]

External Email - Use Caution

Update: I tried running recon-all (5.1, ubuntu 18) on a sample MPRAGE scan and 
got the "mri_convert: segmentation fault (core dumped)" error again. Any 
clarity on this issue would be appreciated.

Thanks,
K
--- Original Message ---
On Thursday, September 14th, 2023 at 10:41 PM, KennethSPrice 
 wrote:

> Howdy yall,
>
> I ran a subject through synthsr (freesurfer 7.4) and am trying to run the 
> output through the freesurfer 5.1 pipeline (the rest of my dataset was 
> processed with 5.1). I am getting the error "Segmentation fault (core 
> dumped)" during the mri_convert step. Any suggestions?
>
> Thanks,
> Ken___
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[Freesurfer] mri_convert: Segmentation fault (core dumped) synthsr scan

[KennethSPrice]

External Email - Use Caution

Howdy yall,

I ran a subject through synthsr (freesurfer 7.4) and am trying to run the 
output through the freesurfer 5.1 pipeline (the rest of my dataset was 
processed with 5.1). I am getting the error "Segmentation fault (core dumped)" 
during the mri_convert step. Any suggestions?

Thanks,
Ken___
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Re: [Freesurfer] mri_convert --conform

[Huang, Yujing]

External Email - Use Caution

Hi Giuseppe,

By default, mri_convert uses trilinear interpolation to resample if necessary.

Option -rt, or --resample_type  can be used 
to change the interpolate method.

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Giuseppe
Sent: Monday, April 24, 2023 12:50 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] mri_convert --conform


External Email - Use Caution
Hello,

Could you please tell me which formula is used by the command "mri_convert 
--conform" to rescale the input image to 0-255. I could not find it.

Thank you,
Giuseppe
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[Freesurfer] mri_convert --conform

[Giuseppe]

External Email - Use Caution

Hello,

Could you please tell me which formula is used by the command "mri_convert
--conform" to rescale the input image to 0-255. I could not find it.

Thank you,
Giuseppe
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Re: [Freesurfer] mri_convert mosaic dicoms

[Douglas N. Greve]

it might be. That override was for a particular experimental case, but 
if it works, it works


On 3/27/2023 2:06 PM, John Anderson wrote:


External Email - Use Caution

Thank you, Dr Greve.  I tried it, but it didn't work. By 'didn't 
work,' I mean that when I visualized the NIfTI file, I saw a line on 
the coronal and sagittal planes, and the whole brain on the axial 
view. I was able to generate a NIfTI image with multiple volumes as 
expected by using the mri_convert command with the --nslices-override 
argument, but I'm not sure if I'm using it correctly.


On Mon, Mar 27, 2023 at 11:19 AM Douglas N. Greve 
 wrote:


Can you try it with --dcm2niix ?

On 3/25/2023 9:43 AM, John Anderson wrote:


External Email - Use Caution

Dear Dr Doug Greeve,
For each participant in my dataset, I have 8 mosaic volumes with
36 slices each. I am trying to convert the DICOM files to Nifti
format using the mri_convert command in FreeSurfer version 7.3.2.
However, the conversion process fails even when using this latest
dev version. To resolve this issue, I attempted to use the
--nslices-override option. It seems working, however, I am unsure
if I used it correctly, and I was not able to find any relevant
examples or guidance on how to use this option in the FreeSurfer
documentation or other websites.

n=({-1..7})
unpacksdcmdir -src ./dicoms/ -targ ./ -scanonly log
for i in $(cat dicomdir.sumfile  | awk '{print $2}'); do
n=$(($n + 1))
mri_convert ./dicoms/$i ASL_$n.nii -odt float --nslices-override
36 -f $n
done

Thanks for guidance,
John

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Re: [Freesurfer] mri_convert mosaic dicoms

[John Anderson]

External Email - Use Caution

Thank you, Dr Greve.  I tried it, but it didn't work. By 'didn't work,' I
mean that when I visualized the NIfTI file, I saw a line on the coronal and
sagittal planes, and the whole brain on the axial view. I was able to
generate a NIfTI image with multiple volumes as expected by using the
mri_convert command with the --nslices-override argument, but I'm not sure
if I'm using it correctly.

On Mon, Mar 27, 2023 at 11:19 AM Douglas N. Greve 
wrote:

> Can you try it with --dcm2niix ?
>
> On 3/25/2023 9:43 AM, John Anderson wrote:
>
> External Email - Use Caution
> Dear Dr Doug Greeve,
> For each participant in my dataset, I have 8 mosaic volumes with 36 slices
> each. I am trying to convert the DICOM files to Nifti format using the
> mri_convert command in FreeSurfer version 7.3.2. However, the conversion
> process fails even when using this latest dev version. To resolve this
> issue, I attempted to use the --nslices-override option. It seems working,
> however, I am unsure if I used it correctly, and I was not able to find any
> relevant examples or guidance on how to use this option in the FreeSurfer
> documentation or other websites.
>
> n=({-1..7})
> unpacksdcmdir -src ./dicoms/ -targ ./ -scanonly log
> for i in $(cat dicomdir.sumfile  | awk '{print $2}'); do
> n=$(($n + 1))
> mri_convert ./dicoms/$i ASL_$n.nii -odt float --nslices-override 36 -f $n
> done
>
> Thanks for guidance,
> John
>
> ___
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Re: [Freesurfer] mri_convert mosaic dicoms

[Douglas N. Greve]

Can you try it with --dcm2niix ?

On 3/25/2023 9:43 AM, John Anderson wrote:


External Email - Use Caution

Dear Dr Doug Greeve,
For each participant in my dataset, I have 8 mosaic volumes with 36 
slices each. I am trying to convert the DICOM files to Nifti format 
using the mri_convert command in FreeSurfer version 7.3.2. However, 
the conversion process fails even when using this latest dev version. 
To resolve this issue, I attempted to use the --nslices-override 
option. It seems working, however, I am unsure if I used it correctly, 
and I was not able to find any relevant examples or guidance on how to 
use this option in the FreeSurfer documentation or other websites.


n=({-1..7})
unpacksdcmdir -src ./dicoms/ -targ ./ -scanonly log
for i in $(cat dicomdir.sumfile  | awk '{print $2}'); do
n=$(($n + 1))
mri_convert ./dicoms/$i ASL_$n.nii -odt float --nslices-override 36 -f $n
done

Thanks for guidance,
John

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[Freesurfer] mri_convert mosaic dicoms

[John Anderson]

External Email - Use Caution

Dear Dr Doug Greeve,
For each participant in my dataset, I have 8 mosaic volumes with 36 slices
each. I am trying to convert the DICOM files to Nifti format using the
mri_convert command in FreeSurfer version 7.3.2. However, the conversion
process fails even when using this latest dev version. To resolve this
issue, I attempted to use the --nslices-override option. It seems working,
however, I am unsure if I used it correctly, and I was not able to find any
relevant examples or guidance on how to use this option in the FreeSurfer
documentation or other websites.

n=({-1..7})
unpacksdcmdir -src ./dicoms/ -targ ./ -scanonly log
for i in $(cat dicomdir.sumfile  | awk '{print $2}'); do
n=$(($n + 1))
mri_convert ./dicoms/$i ASL_$n.nii -odt float --nslices-override 36 -f $n
done

Thanks for guidance,
John
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Re: [Freesurfer] mri_convert mosaic data

[Huang, Yujing]

Hi John,

Can you try dcmunpack (https://surfer.nmr.mgh.harvard.edu/fswiki/dcmunpack)  
instead?

Here is an example usage:

dcmunpack -auto-runseq  -src  -trg  
-no-exit-on-error -dcm2niix

You will find the converted images in .

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of John Anderson
Sent: Thursday, March 23, 2023 12:04 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] mri_convert mosaic data


External Email - Use Caution
Thank you.
I would appreciate feedback from developers on two issues.
1) mri_convert in FS v6 is unable to convert any mosaic DICOMs to Nifti format. 
In FS 7.3.2, mri_convert was able to convert mosaic DICOMs to Nifti in some 
subjects but failed for many others. All subjects were scanned on the same MRI 
scanner with the same acquisition parameters, and I am unable to determine the 
cause of the issue.
2) I have 8 ASL mosaic volumes (36 slices) for each participant in my data. 
When attempting to convert the DICOMs to Nifti using the simple mri_convert 
  command, it fails. Is it correct to apply the 
following steps?

n=({-1..6})
unpacksdcmdir -src ./dicoms/ -targ ./ -scanonly log
for i in $(cat dicomdir.sumfile  | awk '{print $2}'); do
n=$(($n + 1))
mri_convert ./dicoms/$i ASL_$n.nii -odt float --nslices-override 36 -f $n
done

Thank for guidance,
John

On Wed, Mar 15, 2023 at 3:07 PM Huang, Yujing 
mailto:yhuan...@mgh.harvard.edu>> wrote:
Hi John,

I’m assuming all 64 DICOM files are in the same directory.

Which Freesurfer version are you using? If you are using 7.3.2, can you try 
mri_convert -dcm2niix to convert those DICOMs? It will use dcm2niix to convert.

Best,

Yujing

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of John Anderson
Sent: Wednesday, March 15, 2023 1:46 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] mri_convert mosaic data


External Email - Use Caution
Dear Freesurfer,
I have ASL DICOM data from a Siemens scanner in mosaic format.
For each subject, there are 64 DICOM files, which consist of both tags and 
controls.
I would like to convert each individual DICOM into a separate NIfTI file or a 
single 4D NIfTI file ,composed of all 64 dicoms, using the mri_convert. 
However, when I use the command mri_convert input_dicom output_nifti, the 
output does not seem right, as it only displays one slice in the sagittal and 
coronal views. Could you please provide guidance on how to properly convert 
these DICOM files using mri_convert?

Thanks very much
John
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Re: [Freesurfer] mri_convert mosaic data

[John Anderson]

External Email - Use Caution

Thank you.
I would appreciate feedback from developers on two issues.
1) mri_convert in FS v6 is unable to convert any mosaic DICOMs to Nifti
format. In FS 7.3.2, mri_convert was able to convert mosaic DICOMs to Nifti
in some subjects but failed for many others. All subjects were scanned on
the same MRI scanner with the same acquisition parameters, and I am unable
to determine the cause of the issue.
2) I have 8 ASL mosaic volumes (36 slices) for each participant in my data.
When attempting to convert the DICOMs to Nifti using the simple mri_convert
  command, it fails. Is it correct to apply the
following steps?

n=({-1..6})
unpacksdcmdir -src ./dicoms/ -targ ./ -scanonly log
for i in $(cat dicomdir.sumfile  | awk '{print $2}'); do
n=$(($n + 1))
mri_convert ./dicoms/$i ASL_$n.nii -odt float --nslices-override 36 -f $n
done

Thank for guidance,
John

On Wed, Mar 15, 2023 at 3:07 PM Huang, Yujing 
wrote:

> Hi John,
>
>
>
> I’m assuming all 64 DICOM files are in the same directory.
>
>
>
> Which Freesurfer version are you using? If you are using 7.3.2, can you
> try mri_convert -dcm2niix to convert those DICOMs? It will use dcm2niix to
> convert.
>
>
>
> Best,
>
>
>
> Yujing
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *John Anderson
> *Sent:* Wednesday, March 15, 2023 1:46 PM
> *To:* Freesurfer support list 
> *Subject:* [Freesurfer] mri_convert mosaic data
>
>
>
> *External Email - Use Caution*
>
> Dear Freesurfer,
>
> I have ASL DICOM data from a Siemens scanner in mosaic format.
>
> For each subject, there are 64 DICOM files, which consist of both tags and
> controls.
>
> I would like to convert each individual DICOM into a separate NIfTI file
> or a single 4D NIfTI file ,composed of all 64 dicoms, using the
> mri_convert. However, when I use the command mri_convert input_dicom
> output_nifti, the output does not seem right, as it only displays one slice
> in the sagittal and coronal views. Could you please provide guidance on how
> to properly convert these DICOM files using mri_convert?
>
>
>
> Thanks very much
>
> John
> ___
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Re: [Freesurfer] mri_convert mosaic data

[Huang, Yujing]

Hi John,

I’m assuming all 64 DICOM files are in the same directory.

Which Freesurfer version are you using? If you are using 7.3.2, can you try 
mri_convert -dcm2niix to convert those DICOMs? It will use dcm2niix to convert.

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of John Anderson
Sent: Wednesday, March 15, 2023 1:46 PM
To: Freesurfer support list 
Subject: [Freesurfer] mri_convert mosaic data


External Email - Use Caution
Dear Freesurfer,
I have ASL DICOM data from a Siemens scanner in mosaic format.
For each subject, there are 64 DICOM files, which consist of both tags and 
controls.
I would like to convert each individual DICOM into a separate NIfTI file or a 
single 4D NIfTI file ,composed of all 64 dicoms, using the mri_convert. 
However, when I use the command mri_convert input_dicom output_nifti, the 
output does not seem right, as it only displays one slice in the sagittal and 
coronal views. Could you please provide guidance on how to properly convert 
these DICOM files using mri_convert?

Thanks very much
John
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[Freesurfer] mri_convert mosaic data

[John Anderson]

External Email - Use Caution

Dear Freesurfer,
I have ASL DICOM data from a Siemens scanner in mosaic format.
For each subject, there are 64 DICOM files, which consist of both tags and
controls.
I would like to convert each individual DICOM into a separate NIfTI file or
a single 4D NIfTI file ,composed of all 64 dicoms, using the mri_convert.
However, when I use the command mri_convert input_dicom output_nifti, the
output does not seem right, as it only displays one slice in the sagittal
and coronal views. Could you please provide guidance on how to properly
convert these DICOM files using mri_convert?

Thanks very much
John
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Re: [Freesurfer] Freesurfer mri_convert

[Douglas N. Greve]

please send the command line, log file, version of FS, etc

On 3/22/2022 11:59 AM, Zoe O'Brien-Moran wrote:


External Email - Use Caution

Dear FS Experts

I am having continued issues with the mri_normalize function on MPRAGE 
data


I get an error message:
3d normalization pass 1 of 2
error: No such file or directory
error: MRInormFindControlPoints: could not find enough control points
error: No such file or directory
error: MRInormFindControlPoints failed

Can you advise on any reason this may be happening?

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[Freesurfer] Freesurfer mri_convert

[Zoe O'Brien-Moran]

External Email - Use Caution

Dear FS Experts

I am having continued issues with the mri_normalize function on MPRAGE data

I get an error message:
3d normalization pass 1 of 2
error: No such file or directory
error: MRInormFindControlPoints: could not find enough control points
error: No such file or directory
error: MRInormFindControlPoints failed

Can you advise on any reason this may be happening?
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Re: [Freesurfer] mri_convert help w/ GE Genesis files

[Douglas N. Greve]

Have you tried dcm2niix? It's pretty robust

On 6/17/2021 6:59 PM, Christopher Mcnorgan wrote:


External Email - Use Caution

External Email - Use Caution

Hi all,

I’ve been provided with some data collected on a 1.5T GE scanner from 
an old published study. The paper doesn’t indicate the scanner model 
(beyond that it’s a 1.5 GE scanner), but I believe they came from a GE 
Genesis, based on the .MR file extension. I have successfully used 
MRIcro to convert the series of .MR files from the anatomical scan to 
Analyze format, so there’s nothing wrong with the files.


I would prefer to script mri_convert to convert the data, but I am 
having problems doing so, as each of my attempts results in a 
segmentation fault. Files were originally named 1.MR to 
128.MR, and based on the program output prior to the core 
dump, I renamed them so that the file numbers were zero-padded, and 
I’ve tried it with and without the input filetype argument, but I get 
the segmentation fault/core dump either way. The command I’m trying is:


mri_convert -i E11816S5I001.MR -it ge -o T1.nii.gz

This gives me:

reading from E11816S5I001.MR...

fname_format  : 
/home/fruit/music/tmp/E11816/mri/S5/renumbered/E11816S5I%d.MR


fname_format2 : 
/home/fruit/music/tmp/E11816/mri/S5/renumbered/E11816S5I%03d.MR


Segmentation fault (core dumped)

I was hoping someone could point out something that I’m missing.

Thanks for your time. It’s much appreciated.

/**

* Chris McNorgan

* Assistant Professor

* Department of Psychology

* University at Buffalo,

* The State University of New York

* *MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be* http://ccnlab.buffalo.edu/ 



* Office: 716.645.0236

* Lab: 716.645.0222

**/


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[Freesurfer] mri_convert help w/ GE Genesis files

[Christopher Mcnorgan]

External Email - Use Caution

Hi all,
I’ve been provided with some data collected on a 1.5T GE scanner from an old 
published study. The paper doesn’t indicate the scanner model (beyond that it’s 
a 1.5 GE scanner), but I believe they came from a GE Genesis, based on the .MR 
file extension. I have successfully used MRIcro to convert the series of .MR 
files from the anatomical scan to Analyze format, so there’s nothing wrong with 
the files.
I would prefer to script mri_convert to convert the data, but I am having 
problems doing so, as each of my attempts results in a segmentation fault. 
Files were originally named 1.MR to 128.MR, and based on the 
program output prior to the core dump, I renamed them so that the file numbers 
were zero-padded, and I’ve tried it with and without the input filetype 
argument, but I get the segmentation fault/core dump either way. The command 
I’m trying is:
mri_convert -i E11816S5I001.MR -it ge -o T1.nii.gz

This gives me:
reading from E11816S5I001.MR...
fname_format  : /home/fruit/music/tmp/E11816/mri/S5/renumbered/E11816S5I%d.MR
fname_format2 : /home/fruit/music/tmp/E11816/mri/S5/renumbered/E11816S5I%03d.MR
Segmentation fault (core dumped)

I was hoping someone could point out something that I’m missing.

Thanks for your time. It’s much appreciated.

/**
* Chris McNorgan
* Assistant Professor
* Department of Psychology
* University at Buffalo,
* The State University of New York
* 
http://secure-web.cisco.com/11HrmGviCIYIvUr8zM_GIo6mtULm1BjCwyqj-E9atrNMCWUVx3DzJxtlHT7nSoWTbCqLXImR86ivf4fgFR744koZDr3GomqMOIwRQaJEwM6q7N_xxgqyostuCSCRLEVEfoNeBaUe4IHV2PyImUcY4miEBHsxm21KYK1WKxpdJ9SbtI78rco3KjoTfQ6ondBcz6tt7r_zhvrryHCT0R-QQ2BMGFryg2lMwqs5gk39FEc64lwoELi7S4C5RBIAAagPXi2ltigsneoTpjg2foVNNLA/http%3A%2F%2Fccnlab.buffalo.edu%2F
* Office: 716.645.0236
* Lab: 716.645.0222
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Re: [Freesurfer] mri_convert error for creating flat_lh.gii file

[Douglas N. Greve]

Try adding a -p as below (-p indicates that it is a patch)
mris_convert -p lh.full.flat.patch.3d flat_lh.gii

On 4/20/2021 2:50 PM, Suzanne Nie wrote:


External Email - Use Caution

Hello Freesurfer Developers,


I'm attempting to create a full surfaces folder in the filestore based 
on the example, with flat_lh.gii, inflated_lh.gii, pia_lh.gii, 
wm_lh.gii, and those for the right hemisphere in order to use 
cortex.quickshow, plt.show, and cortex.webgl.show.



I used cortex.freesurfer.flatten to create files lh.full.flat.patch.3d 
and rh.full.flat.patch.3d from lh.full.patch.3d that I created from 
making cuts. I want to convert these files to flat_lh.gii, but 
mris_conver gives me segmentation fault errors.




mris_convert lh.full.flat.patch.3d flat_lh.gii

ASSERTION FAILED: 
/Users/developer/space_freesurfer/build/tulum/trunk/developer-7.1.1/utils/mrisurf_metricProperties.cpp:4323 
mris->dist_nsize == 0


ASSERTION FAILED: 
/Users/developer/space_freesurfer/build/tulum/trunk/developer-7.1.1/utils/mrisurf_metricProperties.cpp:4323 
mris->dist_nsize == 0


Segmentation fault: 11


I was unable to find similar issues. If my goal is to display using 
cortex.webgl.show, is creating these files the correct step and if so, 
are there any instructions explaining possible steps?



- Freesurfer Version: freesurfer-darwin-macOS-7.1.1-20200811-8b40551

- Platform: macOS Catalina Version 10.15.7

- Darwin Suzannes-MBP 19.6.0 Darwin Kernel Version 19.6.0: Mon Aug 31 
22:12:52 PDT 2020; root:xnu-6153.141.2~1/RELEASE_X86_64 x86_64


- recon-all.log attached



Thank you,

Suzanne


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Re: [Freesurfer] mri_convert problem

[Hoopes, Andrew]

Have you made sure that you have read permission to open those files? What is 
the output of `ls -l asta.mgh`? And asta.nii doesn’t seem to be a file in your 
working directory.

Best,
Andrew

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Pierpaolo Croce 

Date: Thursday, April 8, 2021 at 11:32 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] mri_convert problem

External Email - Use Caution
Dear List,
I have installed the ubuntu version of freesurfer (creating the VM as in the 
tutorial)
I would like to run the following command:

mri_convert -c -oc 0 0 0 asta.mgh orig.mgz

I always get the error in the screen shot. Can someone help me?
also using asta.nii format
--

Ing. Pierpaolo Croce, PhD.
Institute for Advanced Biomedical Technologies - ITAB
and
Department of Neuroscience and Imaging
University of Chieti "G. D'Annunzio"
Via dei Vestini, 33
66013 Chieti, Italy
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Re: [Freesurfer] mri_convert error: GetSDCMFileInfo(): dcmGetDWIParams() 7

[Hannah Eichhorn]

External Email - Use Caution

Yes, it runs to completion with --no-dwi. And for now, we don't need the
bvals and bvects.  

Thanks a lot for your help! 

On 26.01.2021 16:16, Douglas N. Greve wrote:

> It throws an error when trying to extract the bvals or bvects. Can you try it 
> with --no-dwi and see if it runs to completion? If it does, do you have 
> another way to get the bvals and bvects?
> 
> On 1/26/2021 3:33 AM, Hannah Eichhorn wrote: 
> 
> External Email - Use Caution
> 
> Thanks for your answer! 
> 
> The full command line is: 
> 
> mri_convert 
> /indirect/data1/hannah/Test/RESOLVE_3SCAN_TRACE_TRA_P2_160_ADC_0031/MR.MOCO_TRACOLINE_TEST.0031.0001.2021.01.13.12.54.51.790046.85818469.IMA
>  /indirect/data1/hannah/Test/RESOLVE_3SCAN_TRACE_TRA_P2_160_ADC_0031.nii 
> 
> And the terminal output: 
> 
> mri_convert 
> /indirect/data1/hannah/Test/RESOLVE_3SCAN_TRACE_TRA_P2_160_ADC_0031/MR.MOCO_TRACOLINE_TEST.0031.0001.2021.01.13.12.54.51.790046.85818469.IMA
>  /indirect/data1/hannah/Test/RESOLVE_3SCAN_TRACE_TRA_P2_160_ADC_0031.nii  
> 
> reading from 
> /indirect/data1/hannah/Test/RESOLVE_3SCAN_TRACE_TRA_P2_160_ADC_0031/MR.MOCO_TRACOLINE_TEST.0031.0001.2021.01.13.12.54.51.790046.85818469.IMA...
>  
> 
> INFO: this looks like a dicom, not an old Siemens .ima file, so I'm going to 
> unpack it as a dicom. 
> 
> If this fails, run mri_convert with -it dicom 
> 
> Getting Series No  
> 
> Scanning Directory  
> 
> INFO: Found 29 files in 
> /indirect/data1/hannah/Test/RESOLVE_3SCAN_TRACE_TRA_P2_160_ADC_0031 
> 
> INFO: Scanning for Series Number 31 
> 
> INFO: found 27 files in series 
> 
> INFO: loading series header info. 
> 
> ERROR: GetSDCMFileInfo(): dcmGetDWIParams() 7 
> 
> DICOM File: 
> /indirect/data1/hannah/Test/RESOLVE_3SCAN_TRACE_TRA_P2_160_ADC_0031/MR.MOCO_TRACOLINE_TEST.0031.0001.2021.01.13.12.54.51.790046.85818469.IMA
>  
> 
> break 
> /autofs/space/topaz_001/topaz_nightly_build/trunk/ah221-7.1.1/utils/DICOMRead.cpp:2639
>  
> 
> ERROR: reading 
> /indirect/data1/hannah/Test/RESOLVE_3SCAN_TRACE_TRA_P2_160_ADC_0031/MR.MOCO_TRACOLINE_TEST.0031.0001.2021.01.13.12.54.51.790046.85818469.IMA
>   
> 
> INFO: sorting. 
> 
> Segmentation fault (core dumped) 
> 
> Best regards, 
> 
> Hannah 
> 
> Am 26.01.2021 04:23:58, schrieb Douglas N. Greve: 
> Can you send the full command line and terminal output?
> 
> On 1/22/2021 4:29 AM, Hannah Eichhorn wrote: 
> 
> External Email - Use Caution Dear all, 
> 
> I am trying to convert Dicom volumes from a DWI Siemens sequence into nifty 
> format, but I get the following error when I run the mri_convert Test.IMA 
> Test.nii command: 
> 
> ERROR: GetSDCMFileInfo(): dcmGetDWIParams() 7  
> DICOM File: Test.IMA  
> break 
> /autofs/space/topaz_001/topaz_nightly_build/trunk/ah221-7.1.1/utils/DICOMRead.cpp:2639
>   
> ERROR: reading Test.IMA  
> INFO: sorting.  
> Segmentation fault (core dumped) 
> 
> I have searched the mail archive and didn't find similar errors. Does anyone 
> have any thoughts on how to solve this error? 
> 
> I am using FreeSurfer version: 
> freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 
> 
> Thank you, 
> Hannah Eichhorn 
> 
> ___
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Re: [Freesurfer] mri_convert error: GetSDCMFileInfo(): dcmGetDWIParams() 7

[Douglas N. Greve]

It throws an error when trying to extract the bvals or bvects. Can you 
try it with --no-dwi and see if it runs to completion? If it does, do 
you have another way to get the bvals and bvects?


On 1/26/2021 3:33 AM, Hannah Eichhorn wrote:


External Email - Use Caution

Thanks for your answer!


The full command line is:


mri_convert 
/indirect/data1/hannah/Test/RESOLVE_3SCAN_TRACE_TRA_P2_160_ADC_0031/MR.MOCO_TRACOLINE_TEST.0031.0001.2021.01.13.12.54.51.790046.85818469.IMA 
/indirect/data1/hannah/Test/RESOLVE_3SCAN_TRACE_TRA_P2_160_ADC_0031.nii



And the terminal output:


mri_convert 
/indirect/data1/hannah/Test/RESOLVE_3SCAN_TRACE_TRA_P2_160_ADC_0031/MR.MOCO_TRACOLINE_TEST.0031.0001.2021.01.13.12.54.51.790046.85818469.IMA 
/indirect/data1/hannah/Test/RESOLVE_3SCAN_TRACE_TRA_P2_160_ADC_0031.nii


reading from 
/indirect/data1/hannah/Test/RESOLVE_3SCAN_TRACE_TRA_P2_160_ADC_0031/MR.MOCO_TRACOLINE_TEST.0031.0001.2021.01.13.12.54.51.790046.85818469.IMA...


INFO: this looks like a dicom, not an old Siemens .ima file, so I'm 
going to unpack it as a dicom.


If this fails, run mri_convert with -it dicom

Getting Series No

Scanning Directory

INFO: Found 29 files in 
/indirect/data1/hannah/Test/RESOLVE_3SCAN_TRACE_TRA_P2_160_ADC_0031


INFO: Scanning for Series Number 31

INFO: found 27 files in series

INFO: loading series header info.

ERROR: GetSDCMFileInfo(): dcmGetDWIParams() 7

DICOM File: 
/indirect/data1/hannah/Test/RESOLVE_3SCAN_TRACE_TRA_P2_160_ADC_0031/MR.MOCO_TRACOLINE_TEST.0031.0001.2021.01.13.12.54.51.790046.85818469.IMA


break 
/autofs/space/topaz_001/topaz_nightly_build/trunk/ah221-7.1.1/utils/DICOMRead.cpp:2639


ERROR: reading 
/indirect/data1/hannah/Test/RESOLVE_3SCAN_TRACE_TRA_P2_160_ADC_0031/MR.MOCO_TRACOLINE_TEST.0031.0001.2021.01.13.12.54.51.790046.85818469.IMA 



INFO: sorting.

Segmentation fault (core dumped)


Best regards,

Hannah



Am 26.01.2021 04:23:58, schrieb Douglas N. Greve:

Can you send the full command line and terminal output?

On 1/22/2021 4:29 AM, Hannah Eichhorn wrote:

External Email - Use Caution

Dear all,

I am trying to convert Dicom volumes from a DWI Siemens
sequence into nifty format, but I get the following error when
I run the mri_convert Test.IMA Test.nii command:

ERROR: GetSDCMFileInfo(): dcmGetDWIParams() 7
DICOM File: Test.IMA
break

/autofs/space/topaz_001/topaz_nightly_build/trunk/ah221-7.1.1/utils/DICOMRead.cpp:2639

ERROR: reading Test.IMA
INFO: sorting.
Segmentation fault (core dumped)

I have searched the mail archive and didn't find similar
errors. Does anyone have any thoughts on how to solve this error?

I am using FreeSurfer
version: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551

Thank you,
Hannah Eichhorn

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Re: [Freesurfer] mri_convert error: GetSDCMFileInfo(): dcmGetDWIParams() 7

[Hannah Eichhorn]

External Email - Use Caution

Thanks for your answer!
The full command line is:
mri_convert 
/indirect/data1/hannah/Test/RESOLVE_3SCAN_TRACE_TRA_P2_160_ADC_0031/MR.MOCO_TRACOLINE_TEST.0031.0001.2021.01.13.12.54.51.790046.85818469.IMA
 /indirect/data1/hannah/Test/RESOLVE_3SCAN_TRACE_TRA_P2_160_ADC_0031.nii


And the terminal output:

mri_convert 
/indirect/data1/hannah/Test/RESOLVE_3SCAN_TRACE_TRA_P2_160_ADC_0031/MR.MOCO_TRACOLINE_TEST.0031.0001.2021.01.13.12.54.51.790046.85818469.IMA
 /indirect/data1/hannah/Test/RESOLVE_3SCAN_TRACE_TRA_P2_160_ADC_0031.nii 
reading from 
/indirect/data1/hannah/Test/RESOLVE_3SCAN_TRACE_TRA_P2_160_ADC_0031/MR.MOCO_TRACOLINE_TEST.0031.0001.2021.01.13.12.54.51.790046.85818469.IMA...
INFO: this looks like a dicom, not an old Siemens .ima file, so I'm going to 
unpack it as a dicom.
If this fails, run mri_convert with -it dicom
Getting Series No 
Scanning Directory 
INFO: Found 29 files in 
/indirect/data1/hannah/Test/RESOLVE_3SCAN_TRACE_TRA_P2_160_ADC_0031
INFO: Scanning for Series Number 31
INFO: found 27 files in series
INFO: loading series header info.
ERROR: GetSDCMFileInfo(): dcmGetDWIParams() 7
DICOM File: 
/indirect/data1/hannah/Test/RESOLVE_3SCAN_TRACE_TRA_P2_160_ADC_0031/MR.MOCO_TRACOLINE_TEST.0031.0001.2021.01.13.12.54.51.790046.85818469.IMA
break 
/autofs/space/topaz_001/topaz_nightly_build/trunk/ah221-7.1.1/utils/DICOMRead.cpp:2639
ERROR: reading 
/indirect/data1/hannah/Test/RESOLVE_3SCAN_TRACE_TRA_P2_160_ADC_0031/MR.MOCO_TRACOLINE_TEST.0031.0001.2021.01.13.12.54.51.790046.85818469.IMA
 
INFO: sorting.
Segmentation fault (core dumped)
Best regards,Hannah

Am 26.01.2021 04:23:58, schrieb Douglas N. Greve:

> 

  
  
Can you send the full command line and terminal output?
> 

> 
> On 1/22/2021 4:29 AM, Hannah Eichhorn
  wrote:
> 
> 
> > 
  
  
  
  > > External Email - Use
  Caution> > 
  > > Dear all,> > 
  
> > 
  > > 
  > > I am trying to convert Dicom volumes from a
DWI Siemens sequence into nifty format, but I get the following
error when I run the mri_convert Test.IMA Test.nii command:
> > > > 
  
> > 
  > > 
  > >   > > ERROR: GetSDCMFileInfo():
  dcmGetDWIParams() 7 
> > > > 
  > >   > > DICOM
  File: Test.IMA 
> > > > 
  > >   > > break
/autofs/space/topaz_001/topaz_nightly_build/trunk/ah221-7.1.1/utils/DICOMRead.cpp:2639
 
> > > > 
  > >   > > ERROR:
  reading Test.IMA 
> > > > 
  > >   > > INFO:
  sorting. 
> > > > 
  > >   > > Segmentation
  fault (core dumped)
> > > > 
  
> > 

> > > > 
  > > I have
  searched the mail archive and didn't find similar errors. Does
  anyone have any thoughts on how to solve this error?
> > > > 
  
> > 

> > > > 
  > > I am using
  FreeSurfer version> > : 
freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551
> > > > 
  
> > 

> > > > 
  > > Thank you,
> > > > 
  > > Hannah Eichhorn
> > > > 
  
> > 
  
  > > ___
Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu> > 
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> >  > 
> 

> 
  

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Re: [Freesurfer] mri_convert error: GetSDCMFileInfo(): dcmGetDWIParams() 7

[Douglas N. Greve]

Can you send the full command line and terminal output?

On 1/22/2021 4:29 AM, Hannah Eichhorn wrote:


External Email - Use Caution

​Dear all,

I am trying to convert Dicom volumes from a DWI Siemens sequence into 
nifty format, but I get the following error when I run the mri_convert 
Test.IMA Test.nii command:


ERROR: GetSDCMFileInfo(): dcmGetDWIParams() 7
DICOM File: Test.IMA
break 
/autofs/space/topaz_001/topaz_nightly_build/trunk/ah221-7.1.1/utils/DICOMRead.cpp:2639 


ERROR: reading Test.IMA
INFO: sorting.
Segmentation fault (core dumped)

I have searched the mail archive and didn't find similar errors. Does 
anyone have any thoughts on how to solve this error?


I am using FreeSurfer 
version: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551


Thank you,
Hannah Eichhorn

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[Freesurfer] mri_convert error: GetSDCMFileInfo(): dcmGetDWIParams() 7

[Hannah Eichhorn]

External Email - Use Caution

​Dear all,

I am trying to convert Dicom volumes from a DWI Siemens sequence into nifty 
format, but I get the following error when I run the mri_convert Test.IMA 
Test.nii command:
ERROR: GetSDCMFileInfo(): dcmGetDWIParams() 7 
DICOM File: Test.IMA 
break 
/autofs/space/topaz_001/topaz_nightly_build/trunk/ah221-7.1.1/utils/DICOMRead.cpp:2639
 
ERROR: reading Test.IMA 
INFO: sorting. 
Segmentation fault (core dumped)


I have searched the mail archive and didn't find similar errors. Does anyone 
have any thoughts on how to solve this error?


I am using FreeSurfer version: 
freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551


Thank you,
Hannah Eichhorn

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Re: [Freesurfer] mri_convert error

[Douglas N. Greve]

It looks like it is trying to extract diffusion info. Try running it 
with --no-dwi


On 11/2/2020 5:11 PM, Georgina Angelopoulou wrote:


External Email - Use Caution

Dear Freesurfer Developers,

I am sorry I did not include the error message.
I am attempting to convert some dicom files to mgz via mri_convert 
command. However, for only 5 participants from my cohort I get the 
following error.

Could you please help me to resolve the problem?

(base) Georgias-MBP:HC21 georgina$ mri_convert 
1.3.46.670589.11.38127.5.0.4944.2019102316491068177.dcm 001.mgz
mri_convert.bin 
1.3.46.670589.11.38127.5.0.4944.2019102316491068177.dcm 001.mgz

$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from 1.3.46.670589.11.38127.5.0.4944.2019102316491068177.dcm...
Starting DICOMRead2()
dcmfile = 
/Users/georgina/Downloads/HD/HC21/1.3.46.670589.11.38127.5.0.4944.2019102316491068177.dcm

dcmdir = /Users/georgina/Downloads/HD/HC21
ERROR: GetDICOMInfo(): dcmGetDWIParams() 9
DICOM File: 
/Users/georgina/Downloads/HD/HC21/1.3.46.670589.11.38127.5.0.4944.2019102316491068177.dcm

break DICOMRead.c:5228
Ref Series No = 201
Found 172 files, checking for dicoms
ERROR: GetDICOMInfo(): dcmGetDWIParams() 9
ERROR: GetDICOMInfo(): dcmGetDWIParams() 9
DICOM File: 
/Users/georgina/Downloads/HD/HC21/1.3.46.670589.11.38127.5.0.4944.2019102316491025102.dcm

break DICOMRead.c:5228
First Sorting
Computing Slice Direction
Vs: -0.99478 0.102 0.0033
Vs: -0.994779 0.102 0.0033
Second Sorting
IsDWI = 0, IsPhilipsDWI = 0
Counting frames
nframes = 1
nslices = 82
ndcmfiles = 82
PE Dir =  (dicom read)
CTABreadASCII(/Applications/freesurfer/FreeSurferColorLUT.txt): could 
not open file

Too many open files
ERROR: reading /Applications/freesurfer/FreeSurferColorLUT.txt
Loading pixel data
ERROR: 
/Users/georgina/Downloads/HD/HC21/1.3.46.670589.11.38127.5.0.4944.2019102316490992042.dcm 
is not a dicom file

70092 Requested element (18 9089) not found in DCM_GetElementVM


Thank you in advance,
Georgina


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[Freesurfer] mri_convert error

[Georgina Angelopoulou]

External Email - Use Caution

Dear Freesurfer Developers,

I am sorry I did not include the error message.
I am attempting to convert some dicom files to mgz via mri_convert command.
However, for only 5 participants from my cohort I get the following error.
Could you please help me to resolve the problem?

(base) Georgias-MBP:HC21 georgina$ mri_convert
1.3.46.670589.11.38127.5.0.4944.2019102316491068177.dcm 001.mgz
mri_convert.bin 1.3.46.670589.11.38127.5.0.4944.2019102316491068177.dcm
001.mgz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from 1.3.46.670589.11.38127.5.0.4944.2019102316491068177.dcm...
Starting DICOMRead2()
dcmfile =
/Users/georgina/Downloads/HD/HC21/1.3.46.670589.11.38127.5.0.4944.2019102316491068177.dcm
dcmdir = /Users/georgina/Downloads/HD/HC21
ERROR: GetDICOMInfo(): dcmGetDWIParams() 9
DICOM File:
/Users/georgina/Downloads/HD/HC21/1.3.46.670589.11.38127.5.0.4944.2019102316491068177.dcm
break DICOMRead.c:5228
Ref Series No = 201
Found 172 files, checking for dicoms
ERROR: GetDICOMInfo(): dcmGetDWIParams() 9
ERROR: GetDICOMInfo(): dcmGetDWIParams() 9
DICOM File:
/Users/georgina/Downloads/HD/HC21/1.3.46.670589.11.38127.5.0.4944.2019102316491025102.dcm
break DICOMRead.c:5228
First Sorting
Computing Slice Direction
Vs: -0.99478 0.102 0.0033
Vs: -0.994779 0.102 0.0033
Second Sorting
IsDWI = 0, IsPhilipsDWI = 0
Counting frames
nframes = 1
nslices = 82
ndcmfiles = 82
PE Dir =  (dicom read)
CTABreadASCII(/Applications/freesurfer/FreeSurferColorLUT.txt): could not
open file
Too many open files
ERROR: reading /Applications/freesurfer/FreeSurferColorLUT.txt
Loading pixel data
ERROR:
/Users/georgina/Downloads/HD/HC21/1.3.46.670589.11.38127.5.0.4944.2019102316490992042.dcm
is not a dicom file
   70092 Requested element (18 9089) not found in DCM_GetElementVM


Thank you in advance,
Georgina
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[Freesurfer] mri_convert error

[Georgina Angelopoulou]

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Dear Freesurfer Developers,

Apologies for double posting.
I am attempting to convert some dicom files to mgz via mri_convert command.
However, for only 5 participants from my cohort I get the following error.
Could you please help me to resolve the problem?

Thank you in advance,
Georgina
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Re: [Freesurfer] mri_convert input files

[Douglas N. Greve]

Sorry, we can't convert PAR/REC files.

On 4/8/2020 4:20 AM, Setiaman, N. wrote:


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Hi,

I would like to convert my raw scans to nifty. The scans are made on a 
Philips scanner. I was able to retrieve most of them as DICOM files, 
but some of them are only available as PAR/REC. Does mri_convert also 
handle PAR/REC or can I only convert the DICOMS with this tool?


Best,

Nikita



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[Freesurfer] mri_convert input files

[Setiaman, N.]

External Email - Use Caution

Hi,

I would like to convert my raw scans to nifty. The scans are made on a Philips 
scanner. I was able to retrieve most of them as DICOM files, but some of them 
are only available as PAR/REC. Does mri_convert also handle PAR/REC or can I 
only convert the DICOMS with this tool?

Best,
Nikita

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uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht
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te informeren door het bericht te retourneren. Het Universitair Medisch
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Re: [Freesurfer] mri_convert no scaling

[Bruce Fischl]

Hi Ezequiel

-noscale 1 works in most cases, but here the analyze file itself specifies 
a scalling that is done as part of the reading process. If you want to 
disable it try (in tcsh):


setenv FS_ANALYZE_NO_RESCALE 1

then run mri_convert as before. You should see an addition printout in the 
output saying it is not rescaling


cheers
Bruce




On Wed, 9 Oct 2019, Ezequiel Mikulan wrote:



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Dear All, 
I have a similar problem to the one posted here ( Re: [Freesurfer]
mri_convert scaling ). In my case I'm trying to convert from ANALYZE (.img,
.hdr and .mat) to NIFTI and I need to keep the scale as in the original
file. I've tried the -ns 1 flag but it doesn't work (which is not surprising
as I've seen on the help page that it is for COR). 

The file was originally in NIFTI format and was converted to ANALYZE
(mri_convert), as I had to use a tool that only accepts this format, and now
I'm trying to go back to NIFTI. I would like to know if there is a way of
doing it without rescaling the output. 

These are the contents of the folder:
.
├── CC0061_philips_3_55_F_full_normfilter.hdr
├── CC0061_philips_3_55_F_full_normfilter.img
├── CC0061_philips_3_55_F_full_normfilter.mat

And this is the output of the command call:

$ mri_convert -ns 1 CC0061_philips_3_55_F_full_normfilter.img test.nii
mri_convert.bin -ns 1 CC0061_philips_3_55_F_full_normfilter.img test.nii
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from CC0061_philips_3_55_F_full_normfilter.img...
  analyzeRead() roi_scale   0.003921570
  analyzeRead() scaling by   0.003921570
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (0.984889, -0.156173, 0.0748529)
j_ras = (0.154421, 0.987589, 0.0286842)
k_ras = (-0.0784036, -0.0166919, 0.996782)
writing to test.nii...

Thanks in advance for your time,

Best

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[Freesurfer] mri_convert no scaling

[Ezequiel Mikulan]

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Dear All, 
I have a similar problem to the one posted here ( Re: [Freesurfer] mri_convert 
scaling ). In my case I'm trying to convert from ANALYZE (.img, .hdr and .mat) 
to NIFTI and I need to keep the scale as in the original file. I've tried the 
-ns 1 flag but it doesn't work (which is not surprising as I've seen on the 
help page that it is for COR). 
The file was originally in NIFTI format and was converted to ANALYZE 
(mri_convert), as I had to use a tool that only accepts this format, and now 
I'm trying to go back to NIFTI. I would like to know if there is a way of doing 
it without rescaling the output. 
These are the contents of the folder:.
├── CC0061_philips_3_55_F_full_normfilter.hdr
├── CC0061_philips_3_55_F_full_normfilter.img
├── CC0061_philips_3_55_F_full_normfilter.mat

And this is the output of the command call:
$ mri_convert -ns 1 CC0061_philips_3_55_F_full_normfilter.img test.nii
mri_convert.bin -ns 1 CC0061_philips_3_55_F_full_normfilter.img test.nii
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from CC0061_philips_3_55_F_full_normfilter.img...
  analyzeRead() roi_scale   0.003921570
  analyzeRead() scaling by   0.003921570
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (0.984889, -0.156173, 0.0748529)
j_ras = (0.154421, 0.987589, 0.0286842)
k_ras = (-0.0784036, -0.0166919, 0.996782)
writing to test.nii...

Thanks in advance for your time,
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Re: [Freesurfer] mri_convert for Philips dicoms

[Greve, Douglas N.,Ph.D.]

Try dcm2niix (not part of FS, you'll have to download and install)

On 9/17/19 3:10 PM, Mun, Anna wrote:
> Dear FreeSurfer team,
>
> I am working with data sent to us from other research site. They use 
> Philips scanner and I can not run mri_convert on the dicoms. Is there 
> other way to mri_convert and reconstruct Philips dicoms.
>
> error log is:
>
> WARNING: tag SeriesNumber not found
> WARNING: tag image orientation not found
> ERROR: GetDICOMInfo(): dcmGetDWIParams() 7
>
> break DICOMRead.c:5228
> Ref Series No = 0
> ERROR: bits = 0 not supported.
> Send email to freesurfer@nmr.mgh.harvard.edu
>
>
> Thank you in advance!
>
> Best,
> Anna
>
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[Freesurfer] mri_convert for Philips dicoms

[Mun, Anna]

Dear FreeSurfer team,

I am working with data sent to us from other research site. They use Philips 
scanner and I can not run mri_convert on the dicoms. Is there other way to 
mri_convert and reconstruct Philips dicoms.

error log is:
WARNING: tag SeriesNumber not found
WARNING: tag image orientation not found
ERROR: GetDICOMInfo(): dcmGetDWIParams() 7

break DICOMRead.c:5228
Ref Series No = 0
ERROR: bits = 0 not supported.
Send email to freesurfer@nmr.mgh.harvard.edu

Thank you in advance!

Best,
Anna
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Re: [Freesurfer] mri_convert segmentation fault (core dumped) in v5.3 on centos6

[fsbuild]

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Hello Caspar,
So are you saying that if you run directly from the terminal in bash (or maybe 
in csh with % sign as prompt)
$mri_convert -i inputvolume.mgz--out_orientation LPS-iis .5 
-ijs .5 -iks .5-vs 1.2 1.2 1.2
- that the command works, but it does not work when run from within a csh 
script ?
If you are getting different results from running commands in the 
terminal environment/shell compared to when the same command runs in a 
script, there must be something different between the terminal and the 
script shell environment, e.g. LD_LIBRARY_PATRH, PATH, or something 
getting set differently.
I would try and reproduce the shell environment variable settings that work 
from the terminal in the csh script.
You could try explicitly running the csh script with -xf as arguments (prints 
out what is getting executed and bypasses any startup settings) to see if it 
works differently.  You can replace foo.csh with your script name below.
$ csh -xf foo.csh
Another useful thing to do is to look at all the environment variables getting 
set in the terminal window where the command works, via
$ env | sort
- and compare that with what you see the csh script sets in the output of “csh 
-xf foo.csh”. You can put an “env | sort” command in the csh script just 
before the mri_convert command runs to see the environment (and then compare it 
to the output of :”env | sort” in the terminal window where the command 
works). 

- R.
External Email - Use 
CautionHi!Unfortunately, it turns out that downgrading glibc does not solve 
thisissue, neither with .14 nor with .15 versions.Doug, we are calling 
mri_convert from a csh script, with the followingoptions:mri_convert -i 
inputvolume.mgz \-o outputvolume.nii.gz \--out_orientation LPS \-iis .5 -ijs .5 
-iks .5 \-vs 1.2 1.2 1.2We then simply get segmentation fault (core dumped).It 
seems to work when we run the same command directly in the terminal.CasparAm 
Do., 16. Mai 2019 um 23:10Uhr schrieb Greve, Douglas 
N.,Ph.D.dgr...@mgh.harvard.edu 
mailto:dgr...@mgh.harvard.edu:Can you send the 
command line and full terminal output?On 5/16/19 5:17 AM, 
Caspar M. Schwiedrzik 
wrote:External Email - Use 
CautionHi!We are getting segmentation fault (core dumped) error when trying 
torun mri_convert on NIFTI files. This is running Freesurfer v5.3 onCentos6, 
specifically v1.179.2.7 of mri_convert.I suspect that this has to do with 
libcrypt incompatibilitiesdescribed for other operating systems , e.g., 
here:https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh..harvard.edu_pipermail__freesurfer_2014-2DSeptember_040528.htmld=DwIGaQc=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStgr=sgvCAzCi3iTXkTNRRVMpDnC6tu0lnijYpKXIX_UNme8m=NBmjYrhl1nTR7-ra_mfc3mtbFAElda33iU_qYFc-17ss=hvSTVmJcAZKj26WCCcgZbqDQcLE9GL1yLaGOXIcGBEYe=and
 in the known issues list of v5.3. 
herehttps://urldefense.proofpoint.com/v2/url?u=https-3A__surfer.nmr.mgh.harvard.edu_fswiki_PreviousReleaseNotesd=DwIGaQc=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStgr=sgvCAzCi3iTXkTNRRVMpDnC6tu0lnijYpKXIX_UNme8m=NBmjYrhl1nTR7-ra_mfc3mtbFAElda33iU_qYFc-17ss=PUDfyokNDX6MKj07m6SVKp-n_mHLc-wsBpe1nedrdD8e=.We
 have libcrypt version 2.17 installed and do not have access 
tolibcrypt-2.14.1.so 
http://libcrypt-2..14.1.sohttps://urldefense.proofpoint.com/v2/url?u=http-3A__libcrypt-2D2.14.1.sod=DwIGaQc=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStgr=sgvCAzCi3iTXkTNRRVMpDnC6tu0lnijYpKXIX_UNme8m=NBmjYrhl1nTR7-ra_mfc3mtbFAElda33iU_qYFc-17ss=oWqfVu5YGSWScZMw3Ypfdy53osHoNywLPtAffB75oR8e=.Is
 there a way to get 
libcrypt-2.14.1.sohttp://libcrypt-2.14.1.sohttps://urldefense.proofpoint.com/v2/url?u=http-3A__libcrypt-2D2.14.1.sod=DwIGaQc=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStgr=sgvCAzCi3iTXkTNRRVMpDnC6tu0lnijYpKXIX_UNme8m=NBmjYrhl1nTR7-ra_mfc3mtbFAElda33iU_qYFc-17ss=oWqfVu5YGSWScZMw3Ypfdy53osHoNywLPtAffB75oR8e=from
 you or is there another known workaround (other thenupdating 
toFreesurfer 6)?Thank you very much! 
Caspar___Freesurfer mailing 
listfreesur...@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.eduhttps://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurferd=DwIGaQc=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStgr=sgvCAzCi3iTXkTNRRVMpDnC6tu0lnijYpKXIX_UNme8m=NBmjYrhl1nTR7-ra_mfc3mtbFAElda33iU_qYFc-17ss=HKE_BsPSCQQGF6or1qTbQw7OmHSzKd1zDxWDvkVFR6ke=___Freesurfer
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mailto:Freesurfer@nmr.mgh.harvard.eduhttps://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurferd=DwIGaQc=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStgr=sgvCAzCi3iTXkTNRRVMpDnC6tu0lnijYpKXIX_UNme8m=NBmjYrhl1nTR7-ra_mfc3mtbFAElda33iU_qYFc-17ss=HKE_BsPSCQQGF6or1qTbQw7OmHSzKd1zDxWDvkVFR6ke=Attached
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Re: [Freesurfer] mri_convert segmentation fault (core dumped) in v5.3 on centos6

[Caspar M. Schwiedrzik]

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Hi!
Unfortunately, it turns out that downgrading glibc does not solve this
issue, neither with .14 nor with .15 versions.

Doug, we are calling mri_convert from a csh script, with the following
options:
mri_convert -i inputvolume.mgz \
-o outputvolume.nii.gz \
--out_orientation LPS \
-iis .5 -ijs .5 -iks .5 \
-vs 1.2 1.2 1.2

We then simply get segmentation fault (core dumped).
It seems to work when we run the same command directly in the terminal.
Caspar


Am Do., 16. Mai 2019 um 23:10 Uhr schrieb Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu>:

> Can you send the command line and full terminal output?
>
> On 5/16/19 5:17 AM, Caspar M. Schwiedrzik wrote:
> >
> > External Email - Use Caution
> >
> > Hi!
> > We are getting segmentation fault (core dumped) error when trying to
> > run mri_convert on NIFTI files. This is running Freesurfer v5.3 on
> > Centos6, specifically v1.179.2.7 of mri_convert.
> >
> > I suspect that this has to do with libcrypt incompatibilities
> > described for other operating systems , e.g., here:
> >
> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_pipermail__freesurfer_2014-2DSeptember_040528.html=DwIGaQ=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg=sgvCAzCi3iTXkTNRRVMpDnC6tu0lnijYpKXIX_UNme8=NBmjYrhl1nTR7-ra_mfc3mtbFAElda33iU_qYFc-17s=hvSTVmJcAZKj26WCCcgZbqDQcLE9GL1yLaGOXIcGBEY=
> >
> > and in the known issues list of v5.3. here
> >
> https://urldefense.proofpoint.com/v2/url?u=https-3A__surfer.nmr.mgh.harvard.edu_fswiki_PreviousReleaseNotes=DwIGaQ=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg=sgvCAzCi3iTXkTNRRVMpDnC6tu0lnijYpKXIX_UNme8=NBmjYrhl1nTR7-ra_mfc3mtbFAElda33iU_qYFc-17s=PUDfyokNDX6MKj07m6SVKp-n_mHLc-wsBpe1nedrdD8=
> .
> >
> > We have libcrypt version 2.17 installed and do not have access to
> > libcrypt-2.14.1.so <
> https://urldefense.proofpoint.com/v2/url?u=http-3A__libcrypt-2D2.14.1.so=DwIGaQ=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg=sgvCAzCi3iTXkTNRRVMpDnC6tu0lnijYpKXIX_UNme8=NBmjYrhl1nTR7-ra_mfc3mtbFAElda33iU_qYFc-17s=oWqfVu5YGSWScZMw3Ypfdy53osHoNywLPtAffB75oR8=
> >.
> > Is there a way to get libcrypt-2.14.1.so <
> https://urldefense.proofpoint.com/v2/url?u=http-3A__libcrypt-2D2.14.1.so=DwIGaQ=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg=sgvCAzCi3iTXkTNRRVMpDnC6tu0lnijYpKXIX_UNme8=NBmjYrhl1nTR7-ra_mfc3mtbFAElda33iU_qYFc-17s=oWqfVu5YGSWScZMw3Ypfdy53osHoNywLPtAffB75oR8=>
>
> > from you or is there another known workaround (other then updating to
> > Freesurfer 6)?
> >
> > Thank you very much! Caspar
> >
> >
> > ___
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> > Freesurfer@nmr.mgh.harvard.edu
> >
> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer=DwIGaQ=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg=sgvCAzCi3iTXkTNRRVMpDnC6tu0lnijYpKXIX_UNme8=NBmjYrhl1nTR7-ra_mfc3mtbFAElda33iU_qYFc-17s=HKE_BsPSCQQGF6or1qTbQw7OmHSzKd1zDxWDvkVFR6k=
>
>
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Re: [Freesurfer] mri_convert segmentation fault (core dumped) in v5.3 on centos6

[Greve, Douglas N.,Ph.D.]

Can you send the command line and full terminal output?

On 5/16/19 5:17 AM, Caspar M. Schwiedrzik wrote:
>
> External Email - Use Caution
>
> Hi!
> We are getting segmentation fault (core dumped) error when trying to 
> run mri_convert on NIFTI files. This is running Freesurfer v5.3 on 
> Centos6, specifically v1.179.2.7 of mri_convert.
>
> I suspect that this has to do with libcrypt incompatibilities 
> described for other operating systems , e.g., here: 
> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-September/040528.html
>  
>
> and in the known issues list of v5.3. here 
> https://surfer.nmr.mgh.harvard.edu/fswiki/PreviousReleaseNotes.
>
> We have libcrypt version 2.17 installed and do not have access to 
> libcrypt-2.14.1.so .
> Is there a way to get libcrypt-2.14.1.so  
> from you or is there another known workaround (other then updating to 
> Freesurfer 6)?
>
> Thank you very much! Caspar
>
>
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Re: [Freesurfer] mri_convert segmentation fault (core dumped) in v5.3 on centos6

[fsbuild]

External Email - Use Caution

​Hello Caspar,
So far, I have not found a CentOS rpm with that 2.14 version of libcrypt, but 
you can download the source from the GNU project and try building it on your 
machine with the following steps.
- R.

1) Become root in your terminal window and cd somewhere to download and build

$ su –
$ cd /home/user/Downloads

2) get the source

$ wget http://ftp.gnu.org/gnu/glibc/glibc-2.14.tar.gz
OR
$ curl -O http://ftp.gnu.org/gnu/glibc/glibc-2.14.tar.gz

3) unpack it and cd there

$ tar zxvf glibc-2.14.tar.gz
$ cd glibc-2.14

4) do the build and set it to install into some convenient location, e.g., 
/opt/glibc-2.14

$ mkdir build
$ cd build
$ ../configure --prefix=/opt/glibc-2.14
$ make 

5) If all goes well, then install

$ make install

6) Check that the library is under opt/glibc-2.14/lib and then you can set 
LD_LIBRARY_PATH to reference it

$ export LD_LIBRARY_PATH=/opt/glibc-2.14/lib

On May 16, 2019, at 05:17, Caspar M. Schwiedrzik 
cschwie...@mail.rockefeller.edu 
wrote:External Email - Use 
CautionHi!We are getting 
segmentation fault (core dumped) error when trying to run mri_convert on NIFTI 
files. This is running Freesurfer v5.3 on Centos6, specifically v1.179.2.7 of 
mri_convert.I suspect that this has to do 
withlibcryptincompatibilities described for other operating systems 
, e.g., 
here:https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-September/040528.htmland
 in the known issues list of v5.3. 
herehttps://surfer.nmr.mgh.harvard.edu/fswiki/PreviousReleaseNotes.We
 have libcrypt version 2.17 installed and do not have access 
tolibcrypt-2.14.1.so.Is there a way to 
getlibcrypt-2.14.1.sofrom you or is there another known workaround 
(other then updating to Freesurfer 6)?Thank you very much! 
Caspar___Freesurfer mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer$
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Re: [Freesurfer] mri_convert issues

[Tim Schäfer]

External Email - Use Caution

Dear Jennifer,

if your nifti1 files are named 'brain_nii.hdr' and 'brain_nii.img', try the 
following:

  mri_convert brain_nii --out_type nii brain2.nii

Best,

Tim




> On May 16, 2019 at 12:38 PM jennifer sorinas  wrote:
> 
> 
> External Email - Use Caution
> 
> Dear Tim,
> 
> Thanks for your response. I'm sure that the command is mri-convert (I was 
> using it few months ago without problems). Btw, we are experiencing problems 
> also with the recon-all command at different computers. I don't know which is 
> the error, any more ideas?
> 
> Best,
> Jennifer
> 
> 
> De: freesurfer-boun...@nmr.mgh.harvard.edu 
>  en nombre de Tim Schäfer 
> 
> Enviado: jueves, 16 de mayo de 2019 11:50
> Para: Freesurfer support list
> Asunto: Re: [Freesurfer] mri_convert issues
> 
> External Email - Use Caution
> 
> Dear Jennifer,
> 
> could it be that you are confusing `mri_convert` and `mris_convert` (note the 
> 's')?
> 
> Best,
> 
> Tim
> 
> > On May 16, 2019 at 10:58 AM jennifer sorinas  wrote:
> > I was trying to convert nifti1 files (.hdr and .img) to nii files using the 
> > command:
> > > mri_convert -i input.hdr -it nifti1 -ot nii -o output.nii.gz
> > But this error pop-up:
> > mri_convert.bin: unknown flag '-i input.hdr'
> >
> > The same command was working on my unit a few months ago. Does anybody know 
> > wha's going on?
> >
> > Thank you very much.
> > Best,
> > Jennifer
> > ___
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> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> 
> --
> Dr. Tim Schäfer
> Postdoc Computational Neuroimaging
> Department of Child and Adolescent Psychiatry, Psychosomatics and 
> Psychotherapy
> University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany
> 
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Liebe Grüße,


Tim


-- 
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0176 84273709

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Re: [Freesurfer] mri_convert issues

[Bruce Fischl]

Hi Jennifer

try

 mri_convert -it nifti1  input.img output.nii.gz

you might not need the "-it nifti1"

are you sure it's a nifti and not analyze? You need to be careful you have 
the correct direction cosines to make sure you know which is left and which 
is right. Definitely bring it up in freeview after conversion and make sure 
that the anatomical directions you see agree with what freeview thinks they 
are, but that won't help with left/right unless you have a fiducial in the 
image


cheers
Bruce

On Thu, 16 May 2019, jennifer sorinas wrote:



External Email - Use Caution

Hello,

I was trying to convert nifti1 files (.hdr and .img) to nii files using the 
command:
    > mri_convert -i input.hdr -it nifti1 -ot nii -o output.nii.gz
But this error pop-up:
mri_convert.bin: unknown flag '-i input.hdr'

The same command was working on my unit a few months ago. Does anybody know 
wha's going
on? 

Thank you very much.
Best,
Jennifer

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Re: [Freesurfer] mri_convert issues

[jennifer sorinas]

External Email - Use Caution

Dear Tim,

Thanks for your response. I'm sure that the command is mri-convert (I was using 
it few months ago without problems). Btw, we are experiencing problems also 
with the recon-all command at different computers. I don't know which is the 
error, any more ideas?

Best,
Jennifer


De: freesurfer-boun...@nmr.mgh.harvard.edu 
 en nombre de Tim Schäfer 

Enviado: jueves, 16 de mayo de 2019 11:50
Para: Freesurfer support list
Asunto: Re: [Freesurfer] mri_convert issues

External Email - Use Caution

Dear Jennifer,

could it be that you are confusing `mri_convert` and `mris_convert` (note the 
's')?

Best,

Tim

> On May 16, 2019 at 10:58 AM jennifer sorinas  wrote:
> I was trying to convert nifti1 files (.hdr and .img) to nii files using the 
> command:
> > mri_convert -i input.hdr -it nifti1 -ot nii -o output.nii.gz
> But this error pop-up:
> mri_convert.bin: unknown flag '-i input.hdr'
>
> The same command was working on my unit a few months ago. Does anybody know 
> wha's going on?
>
> Thank you very much.
> Best,
> Jennifer
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--
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Postdoc Computational Neuroimaging
Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy
University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

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Re: [Freesurfer] mri_convert issues

[Tim Schäfer]

External Email - Use Caution

Dear Jennifer,

could it be that you are confusing `mri_convert` and `mris_convert` (note the 
's')?

Best,

Tim

> On May 16, 2019 at 10:58 AM jennifer sorinas  wrote:
> I was trying to convert nifti1 files (.hdr and .img) to nii files using the 
> command:
> > mri_convert -i input.hdr -it nifti1 -ot nii -o output.nii.gz
> But this error pop-up:
> mri_convert.bin: unknown flag '-i input.hdr'
> 
> The same command was working on my unit a few months ago. Does anybody know 
> wha's going on?
> 
> Thank you very much.
> Best,
> Jennifer
> ___
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> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


--
Dr. Tim Schäfer
Postdoc Computational Neuroimaging
Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy
University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

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[Freesurfer] mri_convert segmentation fault (core dumped) in v5.3 on centos6

[Caspar M. Schwiedrzik]

External Email - Use Caution

Hi!
We are getting segmentation fault (core dumped) error when trying to run
mri_convert on NIFTI files. This is running Freesurfer v5.3 on Centos6,
specifically v1.179.2.7 of mri_convert.

I suspect that this has to do with libcrypt incompatibilities described for
other operating systems , e.g., here:
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-September/040528.html
and in the known issues list of v5.3. here
https://surfer.nmr.mgh.harvard.edu/fswiki/PreviousReleaseNotes.

We have libcrypt version 2.17 installed and do not have access to
libcrypt-2.14.1.so.
Is there a way to get libcrypt-2.14.1.so from you or is there another known
workaround (other then updating to Freesurfer 6)?

Thank you very much! Caspar
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[Freesurfer] mri_convert issues

[jennifer sorinas]

External Email - Use Caution

Hello,

I was trying to convert nifti1 files (.hdr and .img) to nii files using the 
command:
> mri_convert -i input.hdr -it nifti1 -ot nii -o output.nii.gz
But this error pop-up:
mri_convert.bin: unknown flag '-i input.hdr'

The same command was working on my unit a few months ago. Does anybody know 
wha's going on?

Thank you very much.
Best,
Jennifer
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Re: [Freesurfer] mri_convert : Error while loading library libGLdispatch.so.0

[Hoopes, Andrew]

Hi Vasudev, are you using an old dev distribution? This was an issue a while 
back, but it’s fixed now.
Andrew

From:  on behalf of Dev vasu 

Reply-To: FS Help 
Date: Thursday, April 25, 2019 at 3:30 PM
To: FS Help 
Subject: [Freesurfer] mri_convert : Error while loading library 
libGLdispatch.so.0


External Email - Use Caution
Dear all,

I am trying to convert .mgz file to nii.gz using mri_convert command

mri_convert filename.mgz filename.nii.gz

but i am getting an error

"mri_convert: error while loading shared libraries: libGLdispatch.so.0: cannot 
open shared object file: No such file or directory "

Thanks
Vasudev
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[Freesurfer] mri_convert : Error while loading library libGLdispatch.so.0

[Dev vasu]

External Email - Use Caution

Dear all,

I am trying to convert .mgz file to nii.gz using mri_convert command

mri_convert filename.mgz filename.nii.gz

but i am getting an error

"mri_convert: error while loading shared libraries: libGLdispatch.so.0:
cannot open shared object file: No such file or directory "

Thanks
Vasudev
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[Freesurfer] mri_convert --in_center

[Song, Da-Yea]

External Email - Use Caution

Hello,

Is it possible to change the origin of the aseg.mgz file? I tried mri_convert 
--in_center -117 -219 145 aseg.mgz new_aseg.img. When I opened the new_aseg.img 
file the origin seems to be at 0 -127 0. Any suggestions would be greatly 
appreciated!

Thank you,
Da-Yea

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Re: [Freesurfer] mri_convert

[Greve, Douglas N.,Ph.D.]

On 2/21/19 12:56 PM, john Anderson wrote:
>
> External Email - Use Caution
>
> Hi Dr Greve,
>
> Thanks for the response.
> yes, I need to extract the acquisition times for kinetic modeling 
> using PET surfer. Please I have two follow-up questions and I 
> appreciate any highlights:
> - Are the acquisition times that PET surfer needs to be included in a 
> file called time.dat can be extracted from the PET DICOM header - tag 
> (0008 ,0013) which labeled "Instance Creation Time" is this the 
> correct tag?
I don't know what tags you need to extract the right numbers. Probably 
not the instance creation time.
> - intensity scaling is not imbedded in the dicom, do you kindly 
> suggest how I can convert the PET DICOMS to nifti?
You can use this version of mri_convert
https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_convert
>
> Thanks so much!
> John
>
>
>
>
> you mean you want the acquisition times to do kinetic modeling? I 
> don't have anything to do that. Also, you should check to see whether 
> your PET has intensity scaling imbedded in the dicom as the v6 
> mri_convert does not handle this properly.
>
>
> On 2/20/19 11:44 AM, john Anderson wrote:
>
> >
>
> > External Email - Use Caution
>
> >
>
> > hi FS experts.
>
> > I would like to inquire about the command mri_ convert I use this
>
> > command to convert fMRI and PET 4D volumes from dicom format to nifti.
>
> >
>
> > Are there any flags that can be used in mri_convert command line to
>
> > enable it to extract a text file contain each series time in seconds?
>
> >
>
> > thanks
>
> > John
>
> >
>
> >
>
> > ___
>
> > Freesurfer mailing list
>
> > Freesurfer@nmr.mgh.harvard.edu 
>
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
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>
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>
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>
>
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Re: [Freesurfer] mri_convert

[john Anderson]

External Email - Use Caution

Hi Dr Greve,

Thanks for the response.
yes, I need to extract the acquisition times for kinetic modeling using PET 
surfer. Please I have two follow-up questions and I appreciate any highlights:
- Are the acquisition times that PET surfer needs to be included in a file 
called time.dat can be extracted from the PET DICOM header - tag (0008 ,0013) 
which labeled "Instance Creation Time" is this the correct tag?
- intensity scaling is not imbedded in the dicom, do you kindly suggest how I 
can convert the PET DICOMS to nifti?

Thanks so much!
John

you mean you want the acquisition times to do kinetic modeling? I don't have 
anything to do that. Also, you should check to see whether your PET has 
intensity scaling imbedded in the dicom as the v6 mri_convert does not handle 
this properly.

On 2/20/19 11:44 AM, john Anderson wrote:

>

> External Email - Use Caution

>

> hi FS experts.

> I would like to inquire about the command mri_ convert I use this

> command to convert fMRI and PET 4D volumes from dicom format to nifti.

>

> Are there any flags that can be used in mri_convert command line to

> enable it to extract a text file contain each series time in seconds?

>

> thanks

> John

>

>

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Re: [Freesurfer] mri_convert

[Greve, Douglas N.,Ph.D.]

you mean you want the acquisition times to do kinetic modeling? I don't 
have anything to do that. Also, you should check to see whether your PET 
has intensity scaling imbedded in the dicom as the v6 mri_convert does 
not handle this properly.

On 2/20/19 11:44 AM, john Anderson wrote:
>
> External Email - Use Caution
>
> hi FS experts.
> I would like to inquire about the command mri_ convert
> I use this command to convert fMRI and PET 4D volumes from dicom 
> format to nifti.
>
> Are there any flags that can be used in mri_convert command line to 
> enable it to extract a text file contain each series time in seconds?
>
> thanks
> John
>
>
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Re: [Freesurfer] mri_convert

[Adam Martersteck]

External Email - Use Caution

mri_convert can do lots of things but I would actually try mri_probedicom
to get the DICOM timings. If you have AFNI installed you could also try
dicom_hinfo which has more examples in the AFNI wiki than mrI_probedicomi.
You could just loop over dicoms writing stdout to a text file.

On Wed, Feb 20, 2019 at 10:45 AM john Anderson 
wrote:

> External Email - Use Caution
>
> hi FS experts.
> I would like to inquire about the command mri_ convert
> I use this command to convert fMRI and PET 4D volumes from dicom format to
> nifti.
>
> Are there any flags that can be used in mri_convert command line to enable
> it to extract a text file contain each series time in seconds?
>
> thanks
> John
>
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[Freesurfer] mri_convert

[john Anderson]

External Email - Use Caution

hi FS experts.
I would like to inquire about the command mri_ convert
I use this command to convert fMRI and PET 4D volumes from dicom format to 
nifti.

Are there any flags that can be used in mri_convert command line to enable it 
to extract a text file contain each series time in seconds?

thanks
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Re: [Freesurfer] mri_convert

[Bruce Fischl]

Hi Nazain

I can't replicate this problem. Can you verify that the aseg.mgz is 
correct? If it is, maybe email me those 3 files as well as the complete 
output of mri_convert?


cheers
Bruce
On Fri, 25 Jan 2019, N Saf wrote:



External Email - Use Caution

Dear Bruce,
I had a problem with bringing aseg.mgz into my subject space and you recommend 
this command before:

mri_convert -rl rawavg.mgz -rt nearest aseg.mgz aseg.resliced.mgz

which perfectly worked for me but now when I want to try it in
 new version6 it does not work and the aseg.resliced file contains just 
corpus callosum!, I don't know which I do wrong because it worked before and still 
work with the analysis which I done with last version. would you please 


help me to figure it out?thank you very much for your help.

best regards,

Nazain

PS:the link of previous mail:https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg50794.html 





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[Freesurfer] mri_convert

[N Saf]

External Email - Use Caution

Dear Bruce,
I had a problem with bringing aseg.mgz into my subject space and you
recommend this command before:

mri_convert -rl rawavg.mgz -rt nearest aseg.mgz aseg.resliced.mgz

which perfectly worked for me but now when I want to try it in
 new version6 it does not work and the aseg.resliced file contains just
corpus callosum!, I don't know which I do wrong because it worked
before and still
work with the analysis which I done with last version. would you please

help me to figure it out?thank you very much for your help.

best regards,

Nazain

PS:the link of previous
mail:https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg50794.html
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[Freesurfer] mri_convert

[Timothy Hendrickson]

External Email - Use Caution

 Hello,

I am working on implementing third party designed code which runs
freesurfer via the containerization tool docker. This code runs fine within
docker so that it is not the problem. I am attempting to run this same code
with a tool named udocker which is a tool that emulates a docker
environment but does not require root user privileges in order to do so.

Anyway long story short when I attempt to run the udocker container of
freesurfer 5.3.0-HCP with the default backend (PRoot) I receive a mmap
error with mri_convert which reads: PROT_EXEC | PROT_WRITE. I am able to
work around this error in certain instances, but that is not important
here. What is important is that when I run a udocker container with
freesurfer 6 mri_convert runs without issue.

My two questions are:

1) What differences exist between mri_convert between freesurfer 6 and
5.3.0 - HCP
2) Is there any way that I can download/install the newer version of
mri_convert used for freesurfer 6 within 5.3.0 - HCP?

-Tim
Timothy Hendrickson
Neuroimaging Analyst/Staff Scientist
University of Minnesota Informatics Institute
University of Minnesota
Bioinformatics M.S. Candidate
Office: 612-624-0783
Mobile: 507-259-3434 (texts okay)
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Re: [Freesurfer] mri_convert trying to find DWI parameters from Philips scans

[Douglas N Greve]

try

export FS_LOAD_DWI=0

(or setenv FS_LOAD_DWI 0 for cshell)


On 01/24/2018 02:44 PM, Rockers, Elijah D. wrote:
> Hello,
>
> I am using mri_convert to convert my standard T1-weighted structural 
> images into nifti format.
>
> The conversion works, but it might be somewhat delayed due to spamming 
> the console with the following message
>
> ERROR: don't know how to get DWI parameters from --Philips Healthcare--
> ERROR: GetDICOMInfo(): dcmGetDWIParams() 1
> DICOM File: 
> sd_withholder/withholder_MRI/scans/1201_T1W_TFE/DICOM/1.3.46.670589.11.42034.5.0.10936.2017012009011821006-1201-95-sktipi.dcm
> break DICOMRead.c:5228
>
> As far as I can tell, it spams this message once for each dicom file 
> in the directory, and there being hundreds or even thousands of dicom 
> files for a single subject, this can get old pretty quick. I think 
> this might be new behavior in freesurfer 6, because I don't recall 
> seeing this with 5.3 (although I could be wrong)
>
> Is there anyway to disable this?
>
> Thanks,
> - Eli
>
> Houston Methodist. Leading Medicine.
>
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> receive for the recipient), please contact the sender and delete all 
> copies of the message. Thank you.
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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[Freesurfer] mri_convert trying to find DWI parameters from Philips scans

[Rockers, Elijah D.]

Hello,

I am using mri_convert to convert my standard T1-weighted structural images 
into nifti format.

The conversion works, but it might be somewhat delayed due to spamming the 
console with the following message

ERROR: don't know how to get DWI parameters from --Philips Healthcare--
ERROR: GetDICOMInfo(): dcmGetDWIParams() 1
DICOM File: 
sd_withholder/withholder_MRI/scans/1201_T1W_TFE/DICOM/1.3.46.670589.11.42034.5.0.10936.2017012009011821006-1201-95-sktipi.dcm
break DICOMRead.c:5228

As far as I can tell, it spams this message once for each dicom file in the 
directory, and there being hundreds or even thousands of dicom files for a 
single subject, this can get old pretty quick. I think this might be new 
behavior in freesurfer 6, because I don't recall seeing this with 5.3 (although 
I could be wrong)

Is there anyway to disable this?

Thanks,
- Eli

Houston Methodist. Leading Medicine. Houston Methodist is ranked by U.S. News & 
World Report as the No. 1 hospital in Texas for patient care. Houston Methodist 
is nationally ranked in 8 specialties and is designated as a Magnet hospital 
for excellence in nursing.  Visit us at  houstonmethodist.org. Follow us at  
twitter.com/MethodistHosp and facebook.com/HoustonMethodist.  
***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist 
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material for the sole use of the intended recipient(s). Any review, use, 
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Re: [Freesurfer] mri_convert partial support of nrrd file format for diffusion MRI data

[Douglas Greve]

no sorry, we have not tried to support nrrd in years, so I'm not 
surprised that it does not output bvals/bvecs



On 11/29/17 8:10 AM, Michael Dayan wrote:

Hi,

I was pleasantly surprised when I discovered that mri_convert could 
convert the nrrd file format (to NIFTI in my case). However for 
diffusion MRI data, while it displays the diffusion gradients 
information on the terminal, it does not create the associated bval 
and bvec files. After looking at the mri_convert command-line usage I 
could not find any option to do so. Would anyone know how to create 
the bval and bvec files?


Best,

Michael


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The information in this e-mail is intended only for the person to whom it is
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] mri_convert partial support of nrrd file format for diffusion MRI data

[Michael Dayan]

Hi,

I was pleasantly surprised when I discovered that mri_convert could convert
the nrrd file format (to NIFTI in my case). However for diffusion MRI data,
while it displays the diffusion gradients information on the terminal, it
does not create the associated bval and bvec files. After looking at the
mri_convert command-line usage I could not find any option to do so. Would
anyone know how to create the bval and bvec files?

Best,

Michael
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] mri_convert: line 3: 38445 Segmentation fault

[Douglas N Greve]

Now that I know what the error and that you are using bash, I can give 
you instructions on what to try next. Try running

unset FS_LOAD_DWI



On 09/14/2017 01:13 AM, M Janani wrote:
> Hi Douglas,
>
>   As you recommended, I ran unsetenv FS_LOAD_DWI command in the terminal, 
> but I got Bash command not found error.
>
>   Could you please help me in resolving this error.
>
> Thanks,
>   Janani
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
> Sent: 13 September 2017 22:44
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] mri_convert: line 3: 38445 Segmentation fault
>
> Hi Janani, if you want help, please provide more complete information.
> Eg, what command was not found? What is the terminal output?
>
>
> On 09/13/2017 07:07 AM, M Janani wrote:
>> No.
>> When we ran the unsetenv FS_LOAD_DWI, we got command not found error.
>>
>> Thanks,
>> Janani
>>
>> -Original Message-
>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N
>> Greve
>> Sent: 12 September 2017 21:42
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] mri_convert: line 3: 38445 Segmentation
>> fault
>>
>> Do you mean that the error is still there even after running the unsetenv 
>> command? And you ran them from the shell, one after the other?
>>
>>
>> On 09/12/2017 02:27 AM, M Janani wrote:
>>> Hi Douglas,
>>>
>>> We tried running this command. But command not found error.
>>>
>>> Thanks,
>>> Janani
>>> 
>>>
>>> 
>>>
>>> -Original Message-
>>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas
>>> N Greve
>>> Sent: 12 September 2017 01:25
>>> To: freesurfer@nmr.mgh.harvard.edu
>>> Subject: Re: [Freesurfer] mri_convert: line 3: 38445 Segmentation
>>> fault
>>>
>>> Try running
>>>
>>> unsetenv FS_LOAD_DWI
>>>
>>>
>>> then re-running recon-all
>>>
>>> On 09/11/2017 12:57 PM, M Janani wrote:
>>>> Hi Team,
>>>>
>>>>Am getting segmentation error during the
>>>> reconstruction process.
>>>>
>>>>Please help in resolving the error.
>>>>
>>>>I have attached log for reference.
>>>>
>>>> Thanks,
>>>>
>>>> Janani
>>>>
>>>>
>>>>
>>>> ::DISCLAIMER::
>>>> 
>>>> --
>>>> 
>>>> --
>>>> 
>>>>
>>>> The contents of this e-mail and any attachment(s) are confidential
>>>> and intended for the named recipient(s) only.
>>>> E-mail transmission is not guaranteed to be secure or error-free as
>>>> information could be intercepted, corrupted, lost, destroyed, arrive
>>>> late or incomplete, or may contain viruses in transmission. The e
>>>> mail and its contents (with or without referred errors) shall
>>>> therefore not attach any liability on the originator or HCL or its 
>>>> affiliates.
>>>> Views or opinions, if any, presented in this email are solely those
>>>> of the author and may not necessarily reflect the views or opinions
>>>> of HCL or its affiliates. Any form of reproduction, dissemination,
>>>> copying, disclosure, modification, distribution and / or publication
>>>> of this message without the prior written consent of authorized
>>>> representative of HCL is strictly prohibited. If you have received
>>>> this email in error please delete it and notify the sender
>>>> immediately.
>>>> Before opening any email and/or attachments, please check them for
>>>> viruses and other defects.
>>>>
>>>> 
>>>> --
>>>> 
>>>> --
>>>> 
>>>>
>>>>
>>>>
>>>> ___
>&

Re: [Freesurfer] mri_convert: line 3: 38445 Segmentation fault

[M Janani]

Hi Douglas,

As you recommended, I ran unsetenv FS_LOAD_DWI command in the terminal, 
but I got Bash command not found error.

Could you please help me in resolving this error.

Thanks,
 Janani

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
Sent: 13 September 2017 22:44
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_convert: line 3: 38445 Segmentation fault

Hi Janani, if you want help, please provide more complete information. 
Eg, what command was not found? What is the terminal output?


On 09/13/2017 07:07 AM, M Janani wrote:
> No.
> When we ran the unsetenv FS_LOAD_DWI, we got command not found error.
>
> Thanks,
> Janani
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N 
> Greve
> Sent: 12 September 2017 21:42
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] mri_convert: line 3: 38445 Segmentation 
> fault
>
> Do you mean that the error is still there even after running the unsetenv 
> command? And you ran them from the shell, one after the other?
>
>
> On 09/12/2017 02:27 AM, M Janani wrote:
>> Hi Douglas,
>>
>>  We tried running this command. But command not found error.
>>
>> Thanks,
>> Janani
>>  
>>
>>  
>>
>> -Original Message-
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas 
>> N Greve
>> Sent: 12 September 2017 01:25
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] mri_convert: line 3: 38445 Segmentation 
>> fault
>>
>> Try running
>>
>> unsetenv FS_LOAD_DWI
>>
>>
>> then re-running recon-all
>>
>> On 09/11/2017 12:57 PM, M Janani wrote:
>>> Hi Team,
>>>
>>>   Am getting segmentation error during the 
>>> reconstruction process.
>>>
>>>   Please help in resolving the error.
>>>
>>>   I have attached log for reference.
>>>
>>> Thanks,
>>>
>>> Janani
>>>
>>>
>>>
>>> ::DISCLAIMER::
>>> 
>>> --
>>> 
>>> --
>>> 
>>>
>>> The contents of this e-mail and any attachment(s) are confidential 
>>> and intended for the named recipient(s) only.
>>> E-mail transmission is not guaranteed to be secure or error-free as 
>>> information could be intercepted, corrupted, lost, destroyed, arrive 
>>> late or incomplete, or may contain viruses in transmission. The e 
>>> mail and its contents (with or without referred errors) shall 
>>> therefore not attach any liability on the originator or HCL or its 
>>> affiliates.
>>> Views or opinions, if any, presented in this email are solely those 
>>> of the author and may not necessarily reflect the views or opinions 
>>> of HCL or its affiliates. Any form of reproduction, dissemination, 
>>> copying, disclosure, modification, distribution and / or publication 
>>> of this message without the prior written consent of authorized 
>>> representative of HCL is strictly prohibited. If you have received 
>>> this email in error please delete it and notify the sender 
>>> immediately.
>>> Before opening any email and/or attachments, please check them for 
>>> viruses and other defects.
>>>
>>> 
>>> --
>>> 
>>> --
>>> 
>>>
>>>
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> Outgoing: 
>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>
>> 

Re: [Freesurfer] mri_convert: line 3: 38445 Segmentation fault

[Douglas N Greve]

Hi Janani, if you want help, please provide more complete information. 
Eg, what command was not found? What is the terminal output?


On 09/13/2017 07:07 AM, M Janani wrote:
> No.
> When we ran the unsetenv FS_LOAD_DWI, we got command not found error.
>
> Thanks,
> Janani
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
> Sent: 12 September 2017 21:42
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] mri_convert: line 3: 38445 Segmentation fault
>
> Do you mean that the error is still there even after running the unsetenv 
> command? And you ran them from the shell, one after the other?
>
>
> On 09/12/2017 02:27 AM, M Janani wrote:
>> Hi Douglas,
>>
>>  We tried running this command. But command not found error.
>>
>> Thanks,
>> Janani
>>  
>>
>>  
>>
>> -Original Message-
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
>> Sent: 12 September 2017 01:25
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] mri_convert: line 3: 38445 Segmentation fault
>>
>> Try running
>>
>> unsetenv FS_LOAD_DWI
>>
>>
>> then re-running recon-all
>>
>> On 09/11/2017 12:57 PM, M Janani wrote:
>>> Hi Team,
>>>
>>>   Am getting segmentation error during the
>>> reconstruction process.
>>>
>>>   Please help in resolving the error.
>>>
>>>   I have attached log for reference.
>>>
>>> Thanks,
>>>
>>> Janani
>>>
>>>
>>>
>>> ::DISCLAIMER::
>>> --
>>> --
>>> 
>>>
>>> The contents of this e-mail and any attachment(s) are confidential and
>>> intended for the named recipient(s) only.
>>> E-mail transmission is not guaranteed to be secure or error-free as
>>> information could be intercepted, corrupted, lost, destroyed, arrive
>>> late or incomplete, or may contain viruses in transmission. The e mail
>>> and its contents (with or without referred errors) shall therefore not
>>> attach any liability on the originator or HCL or its affiliates.
>>> Views or opinions, if any, presented in this email are solely those of
>>> the author and may not necessarily reflect the views or opinions of
>>> HCL or its affiliates. Any form of reproduction, dissemination,
>>> copying, disclosure, modification, distribution and / or publication
>>> of this message without the prior written consent of authorized
>>> representative of HCL is strictly prohibited. If you have received
>>> this email in error please delete it and notify the sender
>>> immediately.
>>> Before opening any email and/or attachments, please check them for
>>> viruses and other defects.
>>>
>>> --
>>> --
>>> 
>>>
>>>
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The information in this e-mail is intended only for the person to whom it is 
>> addressed. If you believe this e-mail was sent to you in error and the 
>> e-mail contains patient information, please contact the Partners Compliance 
>> HelpLine at http://www.partners.org/complianceline . If the e-mail was sent 
>> to you in error but does not contain patient information, please contact the 
>> sender and properly dispose of the e-mail.
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] mri_convert: line 3: 38445 Segmentation fault

[M Janani]

No.
When we ran the unsetenv FS_LOAD_DWI, we got command not found error.

Thanks,
Janani

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
Sent: 12 September 2017 21:42
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_convert: line 3: 38445 Segmentation fault

Do you mean that the error is still there even after running the unsetenv 
command? And you ran them from the shell, one after the other?


On 09/12/2017 02:27 AM, M Janani wrote:
> Hi Douglas,
>
>   We tried running this command. But command not found error.
>
> Thanks,
> Janani
>   
>
>   
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
> Sent: 12 September 2017 01:25
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] mri_convert: line 3: 38445 Segmentation fault
>
> Try running
>
> unsetenv FS_LOAD_DWI
>
>
> then re-running recon-all
>
> On 09/11/2017 12:57 PM, M Janani wrote:
>> Hi Team,
>>
>>  Am getting segmentation error during the
>> reconstruction process.
>>
>>  Please help in resolving the error.
>>
>>  I have attached log for reference.
>>
>> Thanks,
>>
>> Janani
>>
>>
>>
>> ::DISCLAIMER::
>> --
>> --
>> 
>>
>> The contents of this e-mail and any attachment(s) are confidential and
>> intended for the named recipient(s) only.
>> E-mail transmission is not guaranteed to be secure or error-free as
>> information could be intercepted, corrupted, lost, destroyed, arrive
>> late or incomplete, or may contain viruses in transmission. The e mail
>> and its contents (with or without referred errors) shall therefore not
>> attach any liability on the originator or HCL or its affiliates.
>> Views or opinions, if any, presented in this email are solely those of
>> the author and may not necessarily reflect the views or opinions of
>> HCL or its affiliates. Any form of reproduction, dissemination,
>> copying, disclosure, modification, distribution and / or publication
>> of this message without the prior written consent of authorized
>> representative of HCL is strictly prohibited. If you have received
>> this email in error please delete it and notify the sender
>> immediately.
>> Before opening any email and/or attachments, please check them for
>> viruses and other defects.
>>
>> --
>> --
>> 
>>
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it is 
> addressed. If you believe this e-mail was sent to you in error and the e-mail 
> contains patient information, please contact the Partners Compliance HelpLine 
> at http://www.partners.org/complianceline . If the e-mail was sent to you in 
> error but does not contain patient information, please contact the sender and 
> properly dispose of the e-mail.
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] mri_convert: line 3: 38445 Segmentation fault

[Douglas N Greve]

Do you mean that the error is still there even after running the 
unsetenv command? And you ran them from the shell, one after the other?


On 09/12/2017 02:27 AM, M Janani wrote:
> Hi Douglas,
>
>   We tried running this command. But command not found error.
>
> Thanks,
> Janani
>   
>
>   
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
> Sent: 12 September 2017 01:25
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] mri_convert: line 3: 38445 Segmentation fault
>
> Try running
>
> unsetenv FS_LOAD_DWI
>
>
> then re-running recon-all
>
> On 09/11/2017 12:57 PM, M Janani wrote:
>> Hi Team,
>>
>>  Am getting segmentation error during the
>> reconstruction process.
>>
>>  Please help in resolving the error.
>>
>>  I have attached log for reference.
>>
>> Thanks,
>>
>> Janani
>>
>>
>>
>> ::DISCLAIMER::
>> --
>> --
>> 
>>
>> The contents of this e-mail and any attachment(s) are confidential and
>> intended for the named recipient(s) only.
>> E-mail transmission is not guaranteed to be secure or error-free as
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> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
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gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] mri_convert: line 3: 38445 Segmentation fault

[M Janani]

Hi Douglas,

We tried running this command. But command not found error.

Thanks,
Janani




-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
Sent: 12 September 2017 01:25
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_convert: line 3: 38445 Segmentation fault

Try running

unsetenv FS_LOAD_DWI


then re-running recon-all

On 09/11/2017 12:57 PM, M Janani wrote:
>
> Hi Team,
>
> Am getting segmentation error during the 
> reconstruction process.
>
> Please help in resolving the error.
>
> I have attached log for reference.
>
> Thanks,
>
> Janani
>
>
>
> ::DISCLAIMER::
> --
> --
> 
>
> The contents of this e-mail and any attachment(s) are confidential and 
> intended for the named recipient(s) only.
> E-mail transmission is not guaranteed to be secure or error-free as 
> information could be intercepted, corrupted, lost, destroyed, arrive 
> late or incomplete, or may contain viruses in transmission. The e mail 
> and its contents (with or without referred errors) shall therefore not 
> attach any liability on the originator or HCL or its affiliates.
> Views or opinions, if any, presented in this email are solely those of 
> the author and may not necessarily reflect the views or opinions of 
> HCL or its affiliates. Any form of reproduction, dissemination, 
> copying, disclosure, modification, distribution and / or publication 
> of this message without the prior written consent of authorized 
> representative of HCL is strictly prohibited. If you have received 
> this email in error please delete it and notify the sender 
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> Before opening any email and/or attachments, please check them for 
> viruses and other defects.
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Re: [Freesurfer] mri_convert: line 3: 38445 Segmentation fault

[Douglas N Greve]

Try running

unsetenv FS_LOAD_DWI


then re-running recon-all

On 09/11/2017 12:57 PM, M Janani wrote:
>
> Hi Team,
>
> Am getting segmentation error during the 
> reconstruction process.
>
> Please help in resolving the error.
>
> I have attached log for reference.
>
> Thanks,
>
> Janani
>
>
>
> ::DISCLAIMER::
> 
>
> The contents of this e-mail and any attachment(s) are confidential and 
> intended for the named recipient(s) only.
> E-mail transmission is not guaranteed to be secure or error-free as 
> information could be intercepted, corrupted,
> lost, destroyed, arrive late or incomplete, or may contain viruses in 
> transmission. The e mail and its contents
> (with or without referred errors) shall therefore not attach any 
> liability on the originator or HCL or its affiliates.
> Views or opinions, if any, presented in this email are solely those of 
> the author and may not necessarily reflect the
> views or opinions of HCL or its affiliates. Any form of reproduction, 
> dissemination, copying, disclosure, modification,
> distribution and / or publication of this message without the prior 
> written consent of authorized representative of
> HCL is strictly prohibited. If you have received this email in error 
> please delete it and notify the sender immediately.
> Before opening any email and/or attachments, please check them for 
> viruses and other defects.
>
> 
>
>
>
> ___
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-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
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[Freesurfer] mri_convert: line 3: 38445 Segmentation fault

[M Janani]

Hi Team,

Am getting segmentation error during the reconstruction process.

Please help in resolving the error.

I have attached log for reference.

Thanks,
Janani





::DISCLAIMER::


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for the named recipient(s) only.
E-mail transmission is not guaranteed to be secure or error-free as information 
could be intercepted, corrupted,
lost, destroyed, arrive late or incomplete, or may contain viruses in 
transmission. The e mail and its contents
(with or without referred errors) shall therefore not attach any liability on 
the originator or HCL or its affiliates.
Views or opinions, if any, presented in this email are solely those of the 
author and may not necessarily reflect the
views or opinions of HCL or its affiliates. Any form of reproduction, 
dissemination, copying, disclosure, modification,
distribution and / or publication of this message without the prior written 
consent of authorized representative of
HCL is strictly prohibited. If you have received this email in error please 
delete it and notify the sender immediately.
Before opening any email and/or attachments, please check them for viruses and 
other defects.




recon-all.log
Description: recon-all.log
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Re: [Freesurfer] mri_convert

[Douglas Greve]

it could be that the info needed to create the orientation info is not 
in the dicom. You can also try it without the -it dicom. You can also 
specify an orientation like --in_orientation RAS. This will probably be 
wrong, but it will at least let you see the image.



On 7/19/17 8:44 PM, John Anderson wrote:

Dear Dr Bruce,
Thank you very much for your response.
I tried
mri_Convert -i INPUT_FIRST_DICOM -it dicom -ot nii -o OUTPUT_4d.nii

The problem is when I run mri_info on the "OUTPUT_4d.nii" I get the 
following


voxel-to-ras determinant 0
ras to voxel transform:
mat =NULL!
MatrixFree: NULL mat POINTER!

I am not sure what I am doing wrong. So thank you for help
Jon


Sent with ProtonMail <https://protonmail.com> Secure Email.


 Original Message ----
Subject: Re: [Freesurfer] mri_convert
Local Time: July 19, 2017 5:12 PM
UTC Time: July 19, 2017 9:12 PM
From: fis...@nmr.mgh.harvard.edu
To: John Anderson <john.ande...@protonmail.com>, Freesurfer support 
list <freesurfer@nmr.mgh.harvard.edu>


Hi Jon

have you tried mri_convert?

cheers
Bruce
On Wed, 19 Jul 2017, John Anderson wrote:

> Dear Freesurfer,
> Are there any tools in Freesurfer that can help to convert PET 
DICOMs to

> nifti files?
>
> Thank you for your help and for any suggestion
> Jon
>
>
>


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HelpLine at
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dispose of the e-mail.




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Re: [Freesurfer] mri_convert

[John Anderson]

Dear Dr Bruce,
Thank you very much for your response.
I tried
mri_Convert -i INPUT_FIRST_DICOM -it dicom -ot nii -o OUTPUT_4d.nii
The problem is when I run mri_info on the "OUTPUT_4d.nii" I get the following
voxel-to-ras determinant 0
ras to voxel transform:
mat =NULL!
MatrixFree: NULL mat POINTER!
I am not sure what I am doing wrong. So thank you for help
Jon

Sent with [ProtonMail](https://protonmail.com) Secure Email.

>  Original Message 
> Subject: Re: [Freesurfer] mri_convert
> Local Time: July 19, 2017 5:12 PM
> UTC Time: July 19, 2017 9:12 PM
> From: fis...@nmr.mgh.harvard.edu
> To: John Anderson <john.ande...@protonmail.com>, Freesurfer support list 
> <freesurfer@nmr.mgh.harvard.edu>
> Hi Jon
> have you tried mri_convert?
> cheers
> Bruce
> On Wed, 19 Jul 2017, John Anderson wrote:
>> Dear Freesurfer,
>> Are there any tools in Freesurfer that can help to convert PET DICOMs to
>> nifti files?
>>
>> Thank you for your help and for any suggestion
>> Jon
>>
>>
>>
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the e-mail
> contains patient information, please contact the Partners Compliance HelpLine 
> at
> http://www.partners.org/complianceline . If the e-mail was sent to you in 
> error
> but does not contain patient information, please contact the sender and 
> properly
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Re: [Freesurfer] mri_convert

[Bruce Fischl]

Hi Jon

have you tried mri_convert?

cheers
Bruce
On Wed, 19 Jul 2017, John Anderson wrote:

> Dear Freesurfer,
> Are there any tools in Freesurfer that can help to convert PET DICOMs to
> nifti files?
> 
> Thank you for your help and for any suggestion
> Jon
> 
> 
>
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[Freesurfer] mri_convert

[John Anderson]

Dear Freesurfer,
Are there any tools in Freesurfer that can help to convert PET DICOMs to nifti 
files?
Thank you for your help and for any suggestion
Jon___
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Re: [Freesurfer] mri_convert

[John Anderson]

Hi Doug thank you for the quick response!

The source is a Siemens scanner. Data derived from the Spine. I don't know what 
is the optimal way to convert these ima images to nifti

what is the source of the ima file? was it anonymized? You can try something 
like adding

-iid -1 0 0 -ijd 0 1 0 -ikd 0 0 1

but this is just guessing at the orientation

 Original Message 
Subject: mri_convert
Local Time: May 15, 2017 9:58 PM
UTC Time: May 16, 2017 1:58 AM
From: john.ande...@protonmail.com
To: Freesurfer support list 

Dear Freessurfer experts,
i want to convert IMA files to nifti using mri_convert I did the following:

mri_convert 54365413.ima output.nii

I got this error
WARNING: bad orientation matrix (determinant = 0) in nifti1 file ...
... continuing.

if I run mri_info on output.nii I see

voxel-to-ras determinant 0

ras to voxel transform:
mat = NULL!
MatrixFree: NULL mat POINTER!

How can I correctly convert IMA to nifti
Thank you for any suggestion
John___
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Re: [Freesurfer] mri_convert

[Douglas Greve]

what is the source of the ima file? was it anonymized? You can try 
something like adding


-iid -1 0 0 -ijd 0 1 0 -ikd 0 0 1

but this is just guessing at the orientation


On 5/15/17 9:58 PM, John Anderson wrote:

Dear Freessurfer experts,
i want to convert IMA files to nifti using mri_convert I did the 
following:


mri_convert 54365413.ima output.nii

I got this error
WARNING: bad orientation matrix (determinant = 0) in nifti1 file ...
... continuing.

if I run mri_info on output.nii I see

voxel-to-ras determinant 0

ras to voxel transform:
mat = NULL!
MatrixFree: NULL mat POINTER!


How can I correctly convert IMA to nifti
Thank you for any suggestion
John



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[Freesurfer] mri_convert

[John Anderson]

Dear Freessurfer experts,
i want to convert IMA files to nifti using mri_convert I did the following:

mri_convert 54365413.ima output.nii

I got this error
WARNING: bad orientation matrix (determinant = 0) in nifti1 file ...
... continuing.

if I run mri_info on output.nii I see

voxel-to-ras determinant 0

ras to voxel transform:
mat = NULL!
MatrixFree: NULL mat POINTER!

How can I correctly convert IMA to nifti
Thank you for any suggestion
John___
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Re: [Freesurfer] mri_convert : pix vs no pix ?

[Douglas N Greve]

When freesurfer reads in an img/hdr file, it makes assumptions about the 
how the data are oriented, so, implicitly, you are using orientation 
info. If you do not have a .mat file, then you can't change the header, 
so you have to change the pixels


On 05/09/2017 01:45 PM, Shane Schofield wrote:
> Sorry, I don't quite understand yet.. Would the header be important as 
> I am not using img / hdr ? Under what sort of circumstances would pix 
> be favourable? I am using .nii after executing mri_convert to go from 
> img/hdr to nii. I note that pix is used in other older threads too.
>
>
> On Tuesday, May 9, 2017 5:58 PM, Douglas N Greve 
>  wrote:
>
>
> When the pixel  data are flipped, you are actually changing the way that
> the data are stored on disk (while keeping the direction info in the
> header constant).
>
>
> On 05/09/2017 12:52 PM, Shane Schofield wrote:
> > Dear Doug,
> > I am trying to flip some PET images so that they are in the same
> > orientation as the T1.
> > I came across this post
> > http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg29281.html
> > Can you explain what what it means to change the pixel data? Should I
> > use pix or without pix? For context I am working with PET data (in
> > img/hdr formats) that seemed to have been flipped L/R somehow.
> > Thank you.
>
> >
> >
> >
> >
> > ___
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> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> -- 
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu 
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom 
> it is
> addressed. If you believe this e-mail was sent to you in error and the 
> e-mail
> contains patient information, please contact the Partners Compliance 
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you 
> in error
> but does not contain patient information, please contact the sender 
> and properly
> dispose of the e-mail.
>
>
>
>
>
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gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Re: [Freesurfer] mri_convert : pix vs no pix ?

[Shane Schofield]

Sorry, I don't quite understand yet.. Would the header be important as I am not 
using img / hdr ? Under what sort of circumstances would pix be favourable? I 
am using .nii after executing mri_convert to go from img/hdr to nii. I note 
that pix is used in other older threads too. 

On Tuesday, May 9, 2017 5:58 PM, Douglas N Greve 
 wrote:
 

 When the pixel  data are flipped, you are actually changing the way that 
the data are stored on disk (while keeping the direction info in the 
header constant).


On 05/09/2017 12:52 PM, Shane Schofield wrote:
> Dear Doug,
> I am trying to flip some PET images so that they are in the same 
> orientation as the T1.
> I came across this post 
> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg29281.html
> Can you explain what what it means to change the pixel data? Should I 
> use pix or without pix? For context I am working with PET data (in 
> img/hdr formats) that seemed to have been flipped L/R somehow.
> Thank you.
>
>
>
>
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Re: [Freesurfer] mri_convert : pix vs no pix ?

[Douglas N Greve]

When the pixel  data are flipped, you are actually changing the way that 
the data are stored on disk (while keeping the direction info in the 
header constant).


On 05/09/2017 12:52 PM, Shane Schofield wrote:
> Dear Doug,
> I am trying to flip some PET images so that they are in the same 
> orientation as the T1.
> I came across this post 
> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg29281.html
> Can you explain what what it means to change the pixel data? Should I 
> use pix or without pix? For context I am working with PET data (in 
> img/hdr formats) that seemed to have been flipped L/R somehow.
> Thank you.
>
>
>
>
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gr...@nmr.mgh.harvard.edu
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Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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[Freesurfer] mri_convert : pix vs no pix ?

[Shane Schofield]

Dear Doug,I am trying to flip some PET images so that they are in the same 
orientation as the T1.I came across this post 
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg29281.htmlCan you 
explain what what it means to change the pixel data? Should I use pix or 
without pix? For context I am working with PET data (in img/hdr formats) that 
seemed to have been flipped L/R somehow. 
Thank you.


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Re: [Freesurfer] mri_convert: the meaning of the arguments -iid, -ijd, -ikd, -iis, -ijs, and -iks?

[Maria Hakonen]

Many thanks for the answer!

Best,
Maria

2017-04-25 21:05 GMT+03:00 Douglas Greve :

> -i{ijk}s will change the voxel size of the columns, rows, and slices,
> respectively
>
> -i{ijk}d will change the direction cosines of the cols, rows, slices
>
>
>
> On 4/25/17 11:47 AM, Maria Hakonen wrote:
>
> Dear Freesurfer experts,
>
> Could someone please let me know what is the meaning of the arguments
> -iid, -ijd, -ikd, -iis, -ijs, and -iks of mri_covert?
> From the internet and by typing mri_convert on the command line I only
> managed to find the following information:
>
> -iis, --in_i_size 
> -ijs, --in_j_size 
> -iks, --in_k_size 
> -iid, --in_i_direction   
> -ijd, --in_j_direction   
> -ikd, --in_k_direction   
>
> However, I don't still understand what is the effect of those argumnents
> in the following command:
>
> mri_convert gre_000.bfloat data.mgh -iid 1 0 0 -ijd 0 -1 0 -ikd 0 0 1 -iis
> 5 -ijs 5 -iks 5
>
> Are the arguments describing the direction and voxelsize of .bfloat?
>
> Best,
> Maria
>
>
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Re: [Freesurfer] mri_convert: the meaning of the arguments -iid, -ijd, -ikd, -iis, -ijs, and -iks?

[Douglas Greve]

-i{ijk}s will change the voxel size of the columns, rows, and slices, 
respectively


-i{ijk}d will change the direction cosines of the cols, rows, slices



On 4/25/17 11:47 AM, Maria Hakonen wrote:

Dear Freesurfer experts,

Could someone please let me know what is the meaning of the arguments 
-iid, -ijd, -ikd, -iis, -ijs, and -iks of mri_covert?
From the internet and by typing mri_convert on the command line I only 
managed to find the following information:


-iis, --in_i_size 
-ijs, --in_j_size 
-iks, --in_k_size 
-iid, --in_i_direction   
-ijd, --in_j_direction   
-ikd, --in_k_direction   

However, I don't still understand what is the effect of those 
argumnents in the following command:


mri_convert gre_000.bfloat data.mgh -iid 1 0 0 -ijd 0 -1 0 -ikd 0 0 1 
-iis 5 -ijs 5 -iks 5


Are the arguments describing the direction and voxelsize of .bfloat?

Best,
Maria


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[Freesurfer] mri_convert: the meaning of the arguments -iid, -ijd, -ikd, -iis, -ijs, and -iks?

[Maria Hakonen]

Dear Freesurfer experts,

Could someone please let me know what is the meaning of the arguments -iid,
-ijd, -ikd, -iis, -ijs, and -iks of mri_covert?
>From the internet and by typing mri_convert on the command line I only
managed to find the following information:

-iis, --in_i_size 
-ijs, --in_j_size 
-iks, --in_k_size 
-iid, --in_i_direction   
-ijd, --in_j_direction   
-ikd, --in_k_direction   

However, I don't still understand what is the effect of those argumnents in
the following command:

mri_convert gre_000.bfloat data.mgh -iid 1 0 0 -ijd 0 -1 0 -ikd 0 0 1 -iis
5 -ijs 5 -iks 5

Are the arguments describing the direction and voxelsize of .bfloat?

Best,
Maria
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Re: [Freesurfer] mri_convert defaults to trilinear interpolation if "--like" option is used, regardless of "-rt nearest"

[Douglas N Greve]

use mri_vol2vol where you can control the interp. Or, for a binary mask 
or segmentation, use mri_label2vol


On 04/11/2017 03:20 PM, Harris Hoke wrote:
>
> I’m currently running freesurfer 6.0.0, and I’ve run into the same 
> problem described in this thread on the archives 
>  
> . Does anyone know if a fix exists?  I'm trying to move binary parcel 
> files from the SPM default MNI152 space to Freesurfer cvs_avg35_MNI152 
> space.
>
> ~Harris
>
>
>
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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[Freesurfer] mri_convert defaults to trilinear interpolation if "--like" option is used, regardless of "-rt nearest"

[Harris Hoke]

I’m currently running freesurfer 6.0.0, and I’ve run into the same problem
described in this thread on the archives

. Does anyone know if a fix exists?  I'm trying to move binary parcel files
from the SPM default MNI152 space to Freesurfer cvs_avg35_MNI152 space.

~Harris
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Re: [Freesurfer] Mri_convert defaults to trilinear interpolation if "--like" option is used, regardless of "-rt nearest"

[Douglas N Greve]

I don't know if this is fixed or not, but you can use mri_vol2vol with 
the --regheader option and specify the interpolation method with --interp


On 03/29/2017 06:25 PM, Harris Hoke wrote:
>
> I’m currently running freesurfer 6.0.0, and I’ve run into the same 
> problem described in this thread on the archives 
>  
> . Does anyone know if a fix exists?
>
> ~Harris
>
> ​
>
>
> ___
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-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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[Freesurfer] Mri_convert defaults to trilinear interpolation if "--like" option is used, regardless of "-rt nearest"

[Harris Hoke]

I’m currently running freesurfer 6.0.0, and I’ve run into the same problem
described in this thread on the archives

. Does anyone know if a fix exists?

~Harris
​
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Re: [Freesurfer] mri_convert error: \'GetDICOMInfo(): dcmGetDWIParams() 7\' in FS6.0

[Douglas N Greve]

When you were getting the error message, was the program continuing? It 
should have continued normally (though it is not good practice to have 
big ERROR messages scrolling across the screen:)


On 03/01/2017 02:58 PM, Gustav Mårtensson wrote:
>
> Hi,
>
> Yes, the buildstamp says 
> freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c and running 
> Ubuntu 16.04.1 LTS:
>
> $ lsb_release -a
> LSB Version: 
> core-9.20160110ubuntu0.2-amd64:core-9.20160110ubuntu0.2-noarch:security-9.20160110ubuntu0.2-amd64:security-9.20160110ubuntu0.2-noarch
> Distributor ID:Ubuntu
> Description:Ubuntu 16.04.1 LTS
> Release:16.04
> Codename:xenial
>
> Running it on another computer with Ubuntu 14.04 and FS 6.0 produces 
> the same error.
>
> *Gustav Mårtensson* | PhD student
> Division of Clinical Geriatrics
> Department of Neurobiology, Care Sciences and Society
> Karolinska Institutet
>
> On 2017-03-01 19:00, Douglas N Greve wrote:
>> And this is in version 6? What platform are you using?
>>
>>
>> On 03/01/2017 12:07 PM, Gustav Mårtensson wrote:
>>> Hi,
>>>
>>> Yes, running mri_convert
>>> ADNI_032_S_0187_MRMPRAGE__br_raw_20060213164320687_1_S11617_I11073.dcm
>>> dummy.mgh still produces the error
>>>
>>> ERROR: GetDICOMInfo(): dcmGetDWIParams() 7
>>> DICOM File:
>>> /home/gustav/Desktop/0e242a36-5390-4358-9f92-eb9f62c48124/ADNI_032_S_0187_MRMPRAGE__br_raw_20060213164320687_1_S11617_I11073.dcm
>>> break DICOMRead.c:5228
>>>
>>> regardless of if the dicom file is in its own directory or not.
>>>
>>> Best,
>>> Gustav
>>>
>>> On 2017-03-01 17:47, Douglas N Greve wrote:
 Yes. I cannot replicate the error on my end. If you copy that dicom file
 to its own directory and try to convert it, do you get the same error?

 doug

 ps. Please include previous correspondence.


 On 03/01/2017 02:54 AM, Gustav Mårtensson wrote:
> Hi Douglas,
>
> Thank you for your reply! I've attached one of the dicoms that fails.
>
> setenv FS_LOAD_DWI 0 removes the error. Would you recommend doing this
> over replacing the mri_convert binary in FS 6.0 with the one from FS
> 5.3.0.
>
> Best regards,
> Gustav
> It looks like it found something that it thinks is a DWI parameter
> butisn't, and it is causing it to fail. Can you send me one of the
> dicoms?In the mean time, if yousetenv FS_LOAD_DWI 0 then the error should 
> go away
>
> On 2/28/17 8:33 AM, Gustav Mårtensson wrote:
>
>  Hi,
>
>  I have a problem when executing the following command on
>  imagesscanned on 1.5T Philips (Intera) in FS 6.0:recon-all
>  
> -i0e242a36-5390-4358-9f92-eb9f62c48124/ADNI_032_S_0187_MRMPRAGE__br_raw_20060213164320687_1_S11617_I11073.dcm-subjid
>  4450a7a0-27e9-42bc-99ab-1c15519ad9a4 -all -mprage
>  -qcache-hippocampal-subfields-T1 -brainstem-structures -cw256
>
>  which during mri_convert produces the error:
>
>  ERROR: GetDICOMInfo(): dcmGetDWIParams() 7
>
>  DICOMs from other scanners works fine as far as we know.
>  Whenprocessing them through 5.3.0 we didn't get any errors like
>  this,regardless of scanner If we just copy the mri_convert
>  binary file fromFS 5.3.0 to FS 6.0 the errors disappears. Would
>  this be the recommendapproach to solve our issues?We are running
>  on Ubuntu 16.04 LTS with FS
>  versionfreesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c.
>  I'veincluded recon-all.log case it is of interest.
>
>  Thank you for your help!
>
>  --
>  *Gustav Mårtensson* | PhD student
>  Division of Clinical Geriatrics
>  Department of Neurobiology, Care Sciences and Society
>  Karolinska Institutet
>
>
>  ___
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>
> ___ Freesurfer mailing
> listfreesur...@nmr.mgh.harvard.edu  
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer  
>   The
> information in this e-mail is intended only for the person to whom
> it is addressed. If you believe this e-mail was sent to you in error
> and the e-mail contains patient information, please contact the
> Partners Compliance HelpLine at
> http://www.partners.org/complianceline  
>   . If the e-mail was sent to
> you in error but does not contain patient information, please
> contact the sender and properly dispose of the e-mail.
> -- 
> *Gustav Mårtensson* | PhD student
> Division of Clinical Geriatrics
> Department of Neurobiology, 

Re: [Freesurfer] mri_convert error: \'GetDICOMInfo(): dcmGetDWIParams() 7\' in FS6.0

[Douglas N Greve]

And this is in version 6? What platform are you using?


On 03/01/2017 12:07 PM, Gustav Mårtensson wrote:
>
> Hi,
>
> Yes, running mri_convert 
> ADNI_032_S_0187_MRMPRAGE__br_raw_20060213164320687_1_S11617_I11073.dcm
>  
> dummy.mgh still produces the error
>
> ERROR: GetDICOMInfo(): dcmGetDWIParams() 7
> DICOM File: 
> /home/gustav/Desktop/0e242a36-5390-4358-9f92-eb9f62c48124/ADNI_032_S_0187_MRMPRAGE__br_raw_20060213164320687_1_S11617_I11073.dcm
> break DICOMRead.c:5228
>
> regardless of if the dicom file is in its own directory or not.
>
> Best,
> Gustav
>
> On 2017-03-01 17:47, Douglas N Greve wrote:
>> Yes. I cannot replicate the error on my end. If you copy that dicom file
>> to its own directory and try to convert it, do you get the same error?
>>
>> doug
>>
>> ps. Please include previous correspondence.
>>
>>
>> On 03/01/2017 02:54 AM, Gustav Mårtensson wrote:
>>> Hi Douglas,
>>>
>>> Thank you for your reply! I've attached one of the dicoms that fails.
>>>
>>> setenv FS_LOAD_DWI 0 removes the error. Would you recommend doing this
>>> over replacing the mri_convert binary in FS 6.0 with the one from FS
>>> 5.3.0.
>>>
>>> Best regards,
>>> Gustav
>>> It looks like it found something that it thinks is a DWI parameter 
>>> butisn't, and it is causing it to fail. Can you send me one of the 
>>> dicoms?In the mean time, if yousetenv FS_LOAD_DWI 0 then the error should 
>>> go away
>>>
>>> On 2/28/17 8:33 AM, Gustav Mårtensson wrote:
>>>
>>> Hi,
>>>
>>> I have a problem when executing the following command on
>>> imagesscanned on 1.5T Philips (Intera) in FS 6.0:recon-all
>>> 
>>> -i0e242a36-5390-4358-9f92-eb9f62c48124/ADNI_032_S_0187_MRMPRAGE__br_raw_20060213164320687_1_S11617_I11073.dcm-subjid
>>> 4450a7a0-27e9-42bc-99ab-1c15519ad9a4 -all -mprage
>>> -qcache-hippocampal-subfields-T1 -brainstem-structures -cw256
>>>
>>> which during mri_convert produces the error:
>>>
>>> ERROR: GetDICOMInfo(): dcmGetDWIParams() 7
>>>
>>> DICOMs from other scanners works fine as far as we know.
>>> Whenprocessing them through 5.3.0 we didn't get any errors like
>>> this,regardless of scanner If we just copy the mri_convert
>>> binary file fromFS 5.3.0 to FS 6.0 the errors disappears. Would
>>> this be the recommendapproach to solve our issues?We are running
>>> on Ubuntu 16.04 LTS with FS
>>> versionfreesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c.
>>> I'veincluded recon-all.log case it is of interest.
>>>
>>> Thank you for your help!
>>>
>>> --
>>> *Gustav Mårtensson* | PhD student
>>> Division of Clinical Geriatrics
>>> Department of Neurobiology, Care Sciences and Society
>>> Karolinska Institutet
>>>
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>> ___ Freesurfer mailing 
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>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 
>>>  The 
>>> information in this e-mail is intended only for the person to whom 
>>> it is addressed. If you believe this e-mail was sent to you in error 
>>> and the e-mail contains patient information, please contact the 
>>> Partners Compliance HelpLine at 
>>> http://www.partners.org/complianceline 
>>>  . If the e-mail was sent to 
>>> you in error but does not contain patient information, please 
>>> contact the sender and properly dispose of the e-mail.
>>> -- 
>>> *Gustav Mårtensson* | PhD student
>>> Division of Clinical Geriatrics
>>> Department of Neurobiology, Care Sciences and Society
>>> Karolinska Institutet
>>>
>>>
>>>
>>> ___
>>> Karolinska Institutet – a medical university

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] mri_convert error: 'GetDICOMInfo(): dcmGetDWIParams() 7' in FS6.0

[Douglas Greve]

It looks like it found something that it thinks is a DWI parameter but 
isn't, and it is causing it to fail. Can you send me one of the dicoms? 
In the mean time, if you


setenv FS_LOAD_DWI 0

then the error should go away

On 2/28/17 8:33 AM, Gustav Mårtensson wrote:


Hi,

I have a problem when executing the following command on images 
scanned on 1.5T Philips (Intera) in FS 6.0:


recon-all -i 
0e242a36-5390-4358-9f92-eb9f62c48124/ADNI_032_S_0187_MRMPRAGE__br_raw_20060213164320687_1_S11617_I11073.dcm 
-subjid 4450a7a0-27e9-42bc-99ab-1c15519ad9a4 -all -mprage -qcache 
-hippocampal-subfields-T1 -brainstem-structures -cw256


which during mri_convert produces the error:

ERROR: GetDICOMInfo(): dcmGetDWIParams() 7

DICOMs from other scanners works fine as far as we know. When 
processing them through 5.3.0 we didn't get any errors like this, 
regardless of scanner If we just copy the mri_convert binary file from 
FS 5.3.0 to FS 6.0 the errors disappears.  Would this be the recommend 
approach to solve our issues?


We are running on Ubuntu 16.04 LTS with FS version 
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c. I've 
included recon-all.log case it is of interest.


Thank you for your help!

--
*Gustav Mårtensson* | PhD student
Division of Clinical Geriatrics
Department of Neurobiology, Care Sciences and Society
Karolinska Institutet


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Re: [Freesurfer] mri_convert error message

[Bruce Fischl]

Hi Robert

disk space and permissions are really the only two things I can think of. 
Can you try writing it somewhere else? Or using .mgz as output (or .nii 
without the .gz)?

cheers
Bruce

On Wed, 4 Jan 2017, Wujek, Robert 
wrote:

> I'm trying to convert a group of .dcm files to .nii.gz, but I've been getting 
> the following output with an error at the end...
>
> mri_convert IM-0020-0001.dcm example.nii.gz
>
> $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $
>
> reading from IM-0020-0001.dcm...
>
> Starting DICOMRead2()
>
> dcmfile = /Users/Desktop/example/IM-0020-0001.dcm
>
> dcmdir = /Users/Desktop/example
>
> Ref Series No = 23
>
> Found 482 files, checking for dicoms
>
> Found 480 dicom files in series.
>
> First Sorting
>
> Computing Slice Direction
>
> Vs: 0 0 3
>
> Vs: 0 0 1
>
> Second Sorting
>
> Counting frames
>
> nframes = 6
>
> nslices = 80
>
> ndcmfiles = 480
>
> PE Dir = ROW (dicom read)
>
> TransferSyntaxUID: --1.2.840.10008.1.2.1--
>
> jpegUID:   --1.2.840.10008.1.2.4--
>
> Loading pixel data
>
> TR=7584.00, TE=11.10, TI=1500.00, flip angle=111.00
>
> i_ras = (-1, 0, 0)
>
> j_ras = (0, -1, 0)
>
> k_ras = (-0, -0, 1)
>
> writing to example.nii.gz...
>
> niiWrite(): error opening file example.nii.gz
>
> ERROR: failure writing example.nii.gz?
>
> I'm wondering how I should interpret this error. I have disk space, and 
> proper permissions. I also have experience using mri_convert with other 
> projects, so generally speaking, I am capable with this script. I would 
> appreciate any suggestions. Thank you.
>
> -Robert Wujek?
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
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The information in this e-mail is intended only for the person to whom it is
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[Freesurfer] mri_convert error message

[Wujek, Robert]

I'm trying to convert a group of .dcm files to .nii.gz, but I've been getting 
the following output with an error at the end...

mri_convert IM-0020-0001.dcm example.nii.gz

$Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $

reading from IM-0020-0001.dcm...

Starting DICOMRead2()

dcmfile = /Users/Desktop/example/IM-0020-0001.dcm

dcmdir = /Users/Desktop/example

Ref Series No = 23

Found 482 files, checking for dicoms

Found 480 dicom files in series.

First Sorting

Computing Slice Direction

Vs: 0 0 3

Vs: 0 0 1

Second Sorting

Counting frames

nframes = 6

nslices = 80

ndcmfiles = 480

PE Dir = ROW (dicom read)

TransferSyntaxUID: --1.2.840.10008.1.2.1--

jpegUID:   --1.2.840.10008.1.2.4--

Loading pixel data

TR=7584.00, TE=11.10, TI=1500.00, flip angle=111.00

i_ras = (-1, 0, 0)

j_ras = (0, -1, 0)

k_ras = (-0, -0, 1)

writing to example.nii.gz...

niiWrite(): error opening file example.nii.gz

ERROR: failure writing example.nii.gz?

I'm wondering how I should interpret this error. I have disk space, and proper 
permissions. I also have experience using mri_convert with other projects, so 
generally speaking, I am capable with this script. I would appreciate any 
suggestions. Thank you.

-Robert Wujek?


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The information in this e-mail is intended only for the person to whom it is
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Re: [Freesurfer] mri_convert dcm 'Mosaic' 2 mgz

[Douglas N Greve]

sorry, if it has lost critical parameters, then we can't recover from it.


On 12/07/2016 01:20 PM, Marianna Riello wrote:
> Dear FS users,
>
> No I can't run it without anonymization.
> Anyway, I do not know if this can be of any help but here attached you can 
> see the error that stopped the reconstruction when I tried to run the nifti 
> version of the "mosaic' dicom; I transformed the dmc2nii with MRIcron.
>
> Thanks,
> Marianna
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
> Sent: Tuesday, December 6, 2016 2:04 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] mri_convert dcm 'Mosaic' 2 mgz
>
> Not sure. This one did not look like a mosaic (it had 256x256 voxels).
> Can you run it without anonymization?
>
>
> On 12/06/2016 01:40 PM, Marianna Riello wrote:
>> Yeah they do not come directly from the scanner. They are anonymized.
>> The same were the enhanced version of the dicom (with 170 files per dicom) 
>> but these in particular didn't show any error with mri_convert.
>> So why should these mosaic ones show the error?
>>
>> Thanks,
>> Marianna
>>
>> -Original Message-
>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N
>> Greve
>> Sent: Tuesday, December 6, 2016 12:59 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] mri_convert dcm 'Mosaic' 2 mgz
>>
>> This file is missing critical information. Did this come directly from your 
>> scanner or was it changed in some way (eg, anonymized)?
>>
>>
>> On 12/06/2016 10:32 AM, Marianna Riello wrote:
>>> Yes I did it, I used your mail but it gives me an error.
>>> Check attachment.
>>>
>>> -Original Message-
>>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas
>>> Greve
>>> Sent: Tuesday, December 6, 2016 10:23 AM
>>> To: freesurfer@nmr.mgh.harvard.edu
>>> Subject: Re: [Freesurfer] mri_convert dcm 'Mosaic' 2 mgz
>>>
>>> I did not. You should have had an opportunity to enter an email
>>> address of the recipient. You can use my email
>>>
>>>
>>> On 12/5/16 6:35 PM, Marianna Riello wrote:
>>>> I uploaded the dicom mosaic on Martinos Center.
>>>> I am wondering whether you received it
>>>>
>>>> -Original Message-
>>>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>>>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas
>>>> N Greve
>>>> Sent: Monday, December 5, 2016 12:13 PM
>>>> To: freesurfer@nmr.mgh.harvard.edu
>>>> Subject: Re: [Freesurfer] mri_convert dcm 'Mosaic' 2 mgz
>>>>
>>>> Can you upload the dicoms to
>>>> https://gate.nmr.mgh.harvard.edu/filedrop2
>>>>
>>>>
>>>> On 12/05/2016 12:09 PM, Marianna Riello wrote:
>>>>> Dear all,
>>>>>
>>>>> Thank you. I tried but still is showing the same error (check
>>>>> 2Error
>>>>> attachment) Do you have any other suggestions?
>>>>>
>>>>> Thanks in advance,
>>>>> Marianna
>>>>>
>>>>> -Original Message-
>>>>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>>>>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of
>>>>> Douglas N Greve
>>>>> Sent: Monday, December 5, 2016 12:00 PM
>>>>> To: freesurfer@nmr.mgh.harvard.edu
>>>>> Subject: Re: [Freesurfer] mri_convert dcm 'Mosaic' 2 mgz
>>>>>
>>>>> Try not including the "-it dicom" arg and see if that works
>>>>>
>>>>>
>>>>> On 12/05/2016 10:01 AM, Marianna Riello wrote:
>>>>>> Dear all again,
>>>>>>
>>>>>> Thanks for your reply.
>>>>>> Please check the error attached when trying to convert the DICOM Mosaic 
>>>>>> in .mgz file when using mri_convert.
>>>>>>
>>>>>> Thanks in advance,
>>>>>> Marianna
>>>>>>
>>>>>>
>>>>>>
>>>>>> -Original Message-
>>>>>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>>>>>> [mailto:free

Re: [Freesurfer] mri_convert dcm 'Mosaic' 2 mgz

[Marianna Riello]

Dear FS users, 

No I can't run it without anonymization. 
Anyway, I do not know if this can be of any help but here attached you can see 
the error that stopped the reconstruction when I tried to run the nifti version 
of the "mosaic' dicom; I transformed the dmc2nii with MRIcron.

Thanks,
Marianna

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
Sent: Tuesday, December 6, 2016 2:04 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_convert dcm 'Mosaic' 2 mgz

Not sure. This one did not look like a mosaic (it had 256x256 voxels). 
Can you run it without anonymization?


On 12/06/2016 01:40 PM, Marianna Riello wrote:
> Yeah they do not come directly from the scanner. They are anonymized.
> The same were the enhanced version of the dicom (with 170 files per dicom) 
> but these in particular didn't show any error with mri_convert.
> So why should these mosaic ones show the error?
>
> Thanks,
> Marianna
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N 
> Greve
> Sent: Tuesday, December 6, 2016 12:59 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] mri_convert dcm 'Mosaic' 2 mgz
>
> This file is missing critical information. Did this come directly from your 
> scanner or was it changed in some way (eg, anonymized)?
>
>
> On 12/06/2016 10:32 AM, Marianna Riello wrote:
>> Yes I did it, I used your mail but it gives me an error.
>> Check attachment.
>>
>> -Original Message-
>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas 
>> Greve
>> Sent: Tuesday, December 6, 2016 10:23 AM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] mri_convert dcm 'Mosaic' 2 mgz
>>
>> I did not. You should have had an opportunity to enter an email 
>> address of the recipient. You can use my email
>>
>>
>> On 12/5/16 6:35 PM, Marianna Riello wrote:
>>> I uploaded the dicom mosaic on Martinos Center.
>>> I am wondering whether you received it
>>>
>>> -Original Message-
>>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas 
>>> N Greve
>>> Sent: Monday, December 5, 2016 12:13 PM
>>> To: freesurfer@nmr.mgh.harvard.edu
>>> Subject: Re: [Freesurfer] mri_convert dcm 'Mosaic' 2 mgz
>>>
>>> Can you upload the dicoms to
>>> https://gate.nmr.mgh.harvard.edu/filedrop2
>>>
>>>
>>> On 12/05/2016 12:09 PM, Marianna Riello wrote:
>>>> Dear all,
>>>>
>>>> Thank you. I tried but still is showing the same error (check 
>>>> 2Error
>>>> attachment) Do you have any other suggestions?
>>>>
>>>> Thanks in advance,
>>>> Marianna
>>>>
>>>> -Original Message-
>>>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>>>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of 
>>>> Douglas N Greve
>>>> Sent: Monday, December 5, 2016 12:00 PM
>>>> To: freesurfer@nmr.mgh.harvard.edu
>>>> Subject: Re: [Freesurfer] mri_convert dcm 'Mosaic' 2 mgz
>>>>
>>>> Try not including the "-it dicom" arg and see if that works
>>>>
>>>>
>>>> On 12/05/2016 10:01 AM, Marianna Riello wrote:
>>>>> Dear all again,
>>>>>
>>>>> Thanks for your reply.
>>>>> Please check the error attached when trying to convert the DICOM Mosaic 
>>>>> in .mgz file when using mri_convert.
>>>>>
>>>>> Thanks in advance,
>>>>> Marianna
>>>>>
>>>>>
>>>>>
>>>>> -Original Message-
>>>>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>>>>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of 
>>>>> Douglas N Greve
>>>>> Sent: Friday, December 2, 2016 12:17 PM
>>>>> To: freesurfer@nmr.mgh.harvard.edu
>>>>> Subject: Re: [Freesurfer] mri_convert dcm 'Mosaic' 2 mgz
>>>>>
>>>>> It will handle mosaics (as the mosaics that fMRI data will come in).
>>>>> Hard to say what is going on without more specifics (command line, 
>>>>> terminal output)
>>>>>
>>>>>
>>>>&

Re: [Freesurfer] mri_convert dcm 'Mosaic' 2 mgz

[Marianna Riello]

Dear FS users, 

No I can't run it without anonymization. 
Anyway, I do not know if this can be of any help but here attached you can see 
the error that stopped the reconstruction when I tried to run the nifti version 
of the "mosaic' dicom; I transformed the dmc2nii with MRIcron.

Thanks, 
Marianna

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
Sent: Tuesday, December 6, 2016 2:04 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_convert dcm 'Mosaic' 2 mgz

Not sure. This one did not look like a mosaic (it had 256x256 voxels). 
Can you run it without anonymization?


On 12/06/2016 01:40 PM, Marianna Riello wrote:
> Yeah they do not come directly from the scanner. They are anonymized.
> The same were the enhanced version of the dicom (with 170 files per dicom) 
> but these in particular didn't show any error with mri_convert.
> So why should these mosaic ones show the error?
>
> Thanks,
> Marianna
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N 
> Greve
> Sent: Tuesday, December 6, 2016 12:59 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] mri_convert dcm 'Mosaic' 2 mgz
>
> This file is missing critical information. Did this come directly from your 
> scanner or was it changed in some way (eg, anonymized)?
>
>
> On 12/06/2016 10:32 AM, Marianna Riello wrote:
>> Yes I did it, I used your mail but it gives me an error.
>> Check attachment.
>>
>> -Original Message-
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas 
>> Greve
>> Sent: Tuesday, December 6, 2016 10:23 AM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] mri_convert dcm 'Mosaic' 2 mgz
>>
>> I did not. You should have had an opportunity to enter an email 
>> address of the recipient. You can use my email
>>
>>
>> On 12/5/16 6:35 PM, Marianna Riello wrote:
>>> I uploaded the dicom mosaic on Martinos Center.
>>> I am wondering whether you received it
>>>
>>> -Original Message-
>>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas 
>>> N Greve
>>> Sent: Monday, December 5, 2016 12:13 PM
>>> To: freesurfer@nmr.mgh.harvard.edu
>>> Subject: Re: [Freesurfer] mri_convert dcm 'Mosaic' 2 mgz
>>>
>>> Can you upload the dicoms to
>>> https://gate.nmr.mgh.harvard.edu/filedrop2
>>>
>>>
>>> On 12/05/2016 12:09 PM, Marianna Riello wrote:
>>>> Dear all,
>>>>
>>>> Thank you. I tried but still is showing the same error (check 
>>>> 2Error
>>>> attachment) Do you have any other suggestions?
>>>>
>>>> Thanks in advance,
>>>> Marianna
>>>>
>>>> -Original Message-
>>>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>>>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of 
>>>> Douglas N Greve
>>>> Sent: Monday, December 5, 2016 12:00 PM
>>>> To: freesurfer@nmr.mgh.harvard.edu
>>>> Subject: Re: [Freesurfer] mri_convert dcm 'Mosaic' 2 mgz
>>>>
>>>> Try not including the "-it dicom" arg and see if that works
>>>>
>>>>
>>>> On 12/05/2016 10:01 AM, Marianna Riello wrote:
>>>>> Dear all again,
>>>>>
>>>>> Thanks for your reply.
>>>>> Please check the error attached when trying to convert the DICOM Mosaic 
>>>>> in .mgz file when using mri_convert.
>>>>>
>>>>> Thanks in advance,
>>>>> Marianna
>>>>>
>>>>>
>>>>>
>>>>> -Original Message-
>>>>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>>>>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of 
>>>>> Douglas N Greve
>>>>> Sent: Friday, December 2, 2016 12:17 PM
>>>>> To: freesurfer@nmr.mgh.harvard.edu
>>>>> Subject: Re: [Freesurfer] mri_convert dcm 'Mosaic' 2 mgz
>>>>>
>>>>> It will handle mosaics (as the mosaics that fMRI data will come in).
>>>>> Hard to say what is going on without more specifics (command line, 
>>>>> terminal output)
>>>>>
>>>>>
>>>>&

Re: [Freesurfer] mri_convert dcm 'Mosaic' 2 mgz

[Douglas N Greve]

Not sure. This one did not look like a mosaic (it had 256x256 voxels). 
Can you run it without anonymization?


On 12/06/2016 01:40 PM, Marianna Riello wrote:
> Yeah they do not come directly from the scanner. They are anonymized.
> The same were the enhanced version of the dicom (with 170 files per dicom) 
> but these in particular didn't show any error with mri_convert.
> So why should these mosaic ones show the error?
>
> Thanks,
> Marianna
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
> Sent: Tuesday, December 6, 2016 12:59 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] mri_convert dcm 'Mosaic' 2 mgz
>
> This file is missing critical information. Did this come directly from your 
> scanner or was it changed in some way (eg, anonymized)?
>
>
> On 12/06/2016 10:32 AM, Marianna Riello wrote:
>> Yes I did it, I used your mail but it gives me an error.
>> Check attachment.
>>
>> -Original Message-
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas Greve
>> Sent: Tuesday, December 6, 2016 10:23 AM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] mri_convert dcm 'Mosaic' 2 mgz
>>
>> I did not. You should have had an opportunity to enter an email address of 
>> the recipient. You can use my email
>>
>>
>> On 12/5/16 6:35 PM, Marianna Riello wrote:
>>> I uploaded the dicom mosaic on Martinos Center.
>>> I am wondering whether you received it
>>>
>>> -Original Message-
>>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
>>> Sent: Monday, December 5, 2016 12:13 PM
>>> To: freesurfer@nmr.mgh.harvard.edu
>>> Subject: Re: [Freesurfer] mri_convert dcm 'Mosaic' 2 mgz
>>>
>>> Can you upload the dicoms to
>>> https://gate.nmr.mgh.harvard.edu/filedrop2
>>>
>>>
>>> On 12/05/2016 12:09 PM, Marianna Riello wrote:
>>>> Dear all,
>>>>
>>>> Thank you. I tried but still is showing the same error (check 2Error
>>>> attachment) Do you have any other suggestions?
>>>>
>>>> Thanks in advance,
>>>> Marianna
>>>>
>>>> -Original Message-
>>>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>>>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N
>>>> Greve
>>>> Sent: Monday, December 5, 2016 12:00 PM
>>>> To: freesurfer@nmr.mgh.harvard.edu
>>>> Subject: Re: [Freesurfer] mri_convert dcm 'Mosaic' 2 mgz
>>>>
>>>> Try not including the "-it dicom" arg and see if that works
>>>>
>>>>
>>>> On 12/05/2016 10:01 AM, Marianna Riello wrote:
>>>>> Dear all again,
>>>>>
>>>>> Thanks for your reply.
>>>>> Please check the error attached when trying to convert the DICOM Mosaic 
>>>>> in .mgz file when using mri_convert.
>>>>>
>>>>> Thanks in advance,
>>>>> Marianna
>>>>>
>>>>>
>>>>>
>>>>> -Original Message-
>>>>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>>>>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas
>>>>> N Greve
>>>>> Sent: Friday, December 2, 2016 12:17 PM
>>>>> To: freesurfer@nmr.mgh.harvard.edu
>>>>> Subject: Re: [Freesurfer] mri_convert dcm 'Mosaic' 2 mgz
>>>>>
>>>>> It will handle mosaics (as the mosaics that fMRI data will come in).
>>>>> Hard to say what is going on without more specifics (command line,
>>>>> terminal output)
>>>>>
>>>>>
>>>>> On 12/02/2016 10:26 AM, Marianna Riello wrote:
>>>>>> Dear all,
>>>>>>
>>>>>> I am wondering whether mri_convert can compute .mgz files for the
>>>>>> reconstructions with the 'Mosaic Format SIEMENS DICOM files'.
>>>>>>
>>>>>> I have been computing .mgz with the enhanced format .dcm so far, and
>>>>>> it always worked.
>>>>>>
>>>>>> I have used mri_convert to compute .mgz from .nii (I previously
>>>>>> transformed the mosaic .dcm format in nifti 

Re: [Freesurfer] mri_convert dcm 'Mosaic' 2 mgz

[Marianna Riello]

Yeah they do not come directly from the scanner. They are anonymized. 
The same were the enhanced version of the dicom (with 170 files per dicom) but 
these in particular didn't show any error with mri_convert. 
So why should these mosaic ones show the error? 

Thanks, 
Marianna

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
Sent: Tuesday, December 6, 2016 12:59 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_convert dcm 'Mosaic' 2 mgz

This file is missing critical information. Did this come directly from your 
scanner or was it changed in some way (eg, anonymized)?


On 12/06/2016 10:32 AM, Marianna Riello wrote:
> Yes I did it, I used your mail but it gives me an error.
> Check attachment.
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas Greve
> Sent: Tuesday, December 6, 2016 10:23 AM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] mri_convert dcm 'Mosaic' 2 mgz
>
> I did not. You should have had an opportunity to enter an email address of 
> the recipient. You can use my email
>
>
> On 12/5/16 6:35 PM, Marianna Riello wrote:
>> I uploaded the dicom mosaic on Martinos Center.
>> I am wondering whether you received it
>>
>> -Original Message-
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
>> Sent: Monday, December 5, 2016 12:13 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] mri_convert dcm 'Mosaic' 2 mgz
>>
>> Can you upload the dicoms to
>> https://gate.nmr.mgh.harvard.edu/filedrop2
>>
>>
>> On 12/05/2016 12:09 PM, Marianna Riello wrote:
>>> Dear all,
>>>
>>> Thank you. I tried but still is showing the same error (check 2Error
>>> attachment) Do you have any other suggestions?
>>>
>>> Thanks in advance,
>>> Marianna
>>>
>>> -Original Message-
>>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N
>>> Greve
>>> Sent: Monday, December 5, 2016 12:00 PM
>>> To: freesurfer@nmr.mgh.harvard.edu
>>> Subject: Re: [Freesurfer] mri_convert dcm 'Mosaic' 2 mgz
>>>
>>> Try not including the "-it dicom" arg and see if that works
>>>
>>>
>>> On 12/05/2016 10:01 AM, Marianna Riello wrote:
>>>> Dear all again,
>>>>
>>>> Thanks for your reply.
>>>> Please check the error attached when trying to convert the DICOM Mosaic in 
>>>> .mgz file when using mri_convert.
>>>>
>>>> Thanks in advance,
>>>> Marianna
>>>>
>>>>
>>>>
>>>> -Original Message-
>>>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>>>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas
>>>> N Greve
>>>> Sent: Friday, December 2, 2016 12:17 PM
>>>> To: freesurfer@nmr.mgh.harvard.edu
>>>> Subject: Re: [Freesurfer] mri_convert dcm 'Mosaic' 2 mgz
>>>>
>>>> It will handle mosaics (as the mosaics that fMRI data will come in).
>>>> Hard to say what is going on without more specifics (command line,
>>>> terminal output)
>>>>
>>>>
>>>> On 12/02/2016 10:26 AM, Marianna Riello wrote:
>>>>> Dear all,
>>>>>
>>>>> I am wondering whether mri_convert can compute .mgz files for the
>>>>> reconstructions with the 'Mosaic Format SIEMENS DICOM files'.
>>>>>
>>>>> I have been computing .mgz with the enhanced format .dcm so far, and
>>>>> it always worked.
>>>>>
>>>>> I have used mri_convert to compute .mgz from .nii (I previously
>>>>> transformed the mosaic .dcm format in nifti with mricron but the
>>>>> reconstruction failed)
>>>>>
>>>>> Thanks in advance,
>>>>>
>>>>> Marianna
>>>>>
>>>>>
>>>>>
>>>>> ___
>>>>> Freesurfer mailing list
>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>> ___
>>>> Freesurfer mailing list
&

Re: [Freesurfer] mri_convert dcm 'Mosaic' 2 mgz

[Douglas N Greve]

This file is missing critical information. Did this come directly from 
your scanner or was it changed in some way (eg, anonymized)?


On 12/06/2016 10:32 AM, Marianna Riello wrote:
> Yes I did it, I used your mail but it gives me an error.
> Check attachment.
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas Greve
> Sent: Tuesday, December 6, 2016 10:23 AM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] mri_convert dcm 'Mosaic' 2 mgz
>
> I did not. You should have had an opportunity to enter an email address of 
> the recipient. You can use my email
>
>
> On 12/5/16 6:35 PM, Marianna Riello wrote:
>> I uploaded the dicom mosaic on Martinos Center.
>> I am wondering whether you received it
>>
>> -Original Message-
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
>> Sent: Monday, December 5, 2016 12:13 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] mri_convert dcm 'Mosaic' 2 mgz
>>
>> Can you upload the dicoms to
>> https://gate.nmr.mgh.harvard.edu/filedrop2
>>
>>
>> On 12/05/2016 12:09 PM, Marianna Riello wrote:
>>> Dear all,
>>>
>>> Thank you. I tried but still is showing the same error (check 2Error
>>> attachment) Do you have any other suggestions?
>>>
>>> Thanks in advance,
>>> Marianna
>>>
>>> -Original Message-
>>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N
>>> Greve
>>> Sent: Monday, December 5, 2016 12:00 PM
>>> To: freesurfer@nmr.mgh.harvard.edu
>>> Subject: Re: [Freesurfer] mri_convert dcm 'Mosaic' 2 mgz
>>>
>>> Try not including the "-it dicom" arg and see if that works
>>>
>>>
>>> On 12/05/2016 10:01 AM, Marianna Riello wrote:
>>>> Dear all again,
>>>>
>>>> Thanks for your reply.
>>>> Please check the error attached when trying to convert the DICOM Mosaic in 
>>>> .mgz file when using mri_convert.
>>>>
>>>> Thanks in advance,
>>>> Marianna
>>>>
>>>>
>>>>
>>>> -Original Message-
>>>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>>>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas
>>>> N Greve
>>>> Sent: Friday, December 2, 2016 12:17 PM
>>>> To: freesurfer@nmr.mgh.harvard.edu
>>>> Subject: Re: [Freesurfer] mri_convert dcm 'Mosaic' 2 mgz
>>>>
>>>> It will handle mosaics (as the mosaics that fMRI data will come in).
>>>> Hard to say what is going on without more specifics (command line,
>>>> terminal output)
>>>>
>>>>
>>>> On 12/02/2016 10:26 AM, Marianna Riello wrote:
>>>>> Dear all,
>>>>>
>>>>> I am wondering whether mri_convert can compute .mgz files for the
>>>>> reconstructions with the 'Mosaic Format SIEMENS DICOM files'.
>>>>>
>>>>> I have been computing .mgz with the enhanced format .dcm so far, and
>>>>> it always worked.
>>>>>
>>>>> I have used mri_convert to compute .mgz from .nii (I previously
>>>>> transformed the mosaic .dcm format in nifti with mricron but the
>>>>> reconstruction failed)
>>>>>
>>>>> Thanks in advance,
>>>>>
>>>>> Marianna
>>>>>
>>>>>
>>>>>
>>>>> ___
>>>>> Freesurfer mailing list
>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>> ___
>>>> Freesurfer mailing list
>>>> Freesurfer@nmr.mgh.harvard.edu
>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>> --
>>> Douglas N. Greve, Ph.D.
>>> MGH-NMR Center
>>> gr...@nmr.mgh.harvard.edu
>>> Phone Number: 617-724-2358
>>> Fax: 617-726-7422
>>>
>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>>> Outgoing:
>&g